2V6G
Structure of Progesterone 5beta-Reductase from Digitalis Lanata in complex with NADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.8 | CONTAINERLESS BATCH METHOD: 300 MICROL OF HIGH-DENSITY SILICON OIL WAS TRANSFERRED INTO A WELL OF A CELL CULTURE PLATE AND OVER-LAID WITH 500 MICROL OF REGULAR SILICON OIL. AT THE INTERFACE BETWEEN THE TWO LIQUIDS A DROPLET WAS DEPOSITED THAT WAS OBTAINED BY MIXING 0.4 MICROL OF H2O, 2.2 MICROL OF 5BETA-POR SOLUTION WITH NADP AND PROGESTERONE ADDED AND 1.8 MICROL OF A CRYSTALLIZATION SOLUTION CONSISTING OF 22.9 % MPD, 3.5 % PEG 8000, 0.05 M SODIUM ACETATE, 0.02 M CACL2, PH 5.8. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 63.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.59 | α = 90 |
b = 78.59 | β = 90 |
c = 178.1 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | MIRRORS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.3 | 40 | 99.9 | 0.08 | 26 | 14.3 | 25629 | 3 | 49.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.3 | 2.4 | 100 | 0.74 | 4.6 | 14.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | NADP FREE STRUCTURE | 2.3 | 39.34 | 23072 | 2557 | 100 | 0.175 | 0.171 | 0.212 | RANDOM | 39.24 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.25 | -0.25 | 0.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.328 |
r_dihedral_angle_3_deg | 15.913 |
r_dihedral_angle_4_deg | 14.586 |
r_dihedral_angle_1_deg | 6.167 |
r_scangle_it | 2.095 |
r_scbond_it | 1.415 |
r_angle_refined_deg | 1.343 |
r_angle_other_deg | 0.996 |
r_mcangle_it | 0.862 |
r_mcbond_it | 0.473 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2889 |
Nucleic Acid Atoms | |
Solvent Atoms | 157 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |