4QRB
Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 289 | 0.02 M calcium chloride, 0.1 M sodium acetate buffer (pH 4.6 to 5), and 30% methyl-2,4-pentanediol (v/v), VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.33 | α = 90 |
b = 66.459 | β = 90 |
c = 206.865 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 120 | CCD | ADSC QUANTUM 4r | 2012-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
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 | 1.64 | 42.52 | 99 | 0.0303 | 19.85 | 48214 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.64 | 42.52 | 45715 | 2431 | 98.94 | 0.21543 | 0.21431 | 0.23605 | RANDOM | 27.29 |
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] | |
0.05 | -0.1 | 0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.205 |
r_dihedral_angle_4_deg | 18.161 |
r_dihedral_angle_3_deg | 14.674 |
r_dihedral_angle_1_deg | 7.594 |
r_angle_refined_deg | 2.275 |
r_angle_other_deg | 0.991 |
r_chiral_restr | 0.14 |
r_bond_refined_d | 0.022 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2554 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |