1RKM
STRUCTURE OF OPPA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OLB | OLIGOPEPTIDE BINDING PROTEIN, PDB CODE 2OLB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 3M (NH4)2SO4, 0.1M HEPES PH7.5, 0.2M NACL AND 20MG/ML OPPA |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.22 | 61.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.84 | α = 90 |
b = 97.84 | β = 90 |
c = 137.21 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | 298 | IMAGE PLATE | MARRESEARCH | 1995-07-08 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.5 | SRS | PX9.5 |
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 | 2.4 | 15 | 99.3 | 0.103 | 6.8 | 3.7 | 30015 | 34.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.4 | 2.53 | 99.5 | 0.457 | 1.6 | 3.7 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | OLIGOPEPTIDE BINDING PROTEIN, PDB CODE 2OLB | 2.4 | 20 | 30015 | 99.3 | 0.191 | 0.247 | RANDOM | 28.9 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
p_transverse_tor | 30.2 |
p_staggered_tor | 21.8 |
p_planar_tor | 5.4 |
p_scangle_it | 4.396 |
p_mcangle_it | 3.101 |
p_scbond_it | 2.937 |
p_mcbond_it | 2.106 |
p_multtor_nbd | 0.263 |
p_singtor_nbd | 0.194 |
p_xyhbond_nbd | 0.182 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4190 |
Nucleic Acid Atoms | |
Solvent Atoms | 125 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
ROTAVATA | data reduction |
Agrovata | data reduction |
AMoRE | phasing |
REFMAC | refinement |
CCP4 | data scaling |
ROTAVATA | data scaling |