1YQG
Crystal structure of a pyrroline-5-carboxylate reductase from neisseria meningitides mc58
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | AMMONIUM SULFATE, HEPES, PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 51.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 89.526 | ¦Á = 90 |
b = 49.845 | ¦Â = 90 |
c = 65.534 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | CUSTOM-MADE | 2004-07-23 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97984, 0.97970 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.61 | 50 | 69 | 0.102 | 24.66 | 9.5 | 38574 | 26616 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.61 | 1.67 | 0.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.9 | 50 | 22585 | 22303 | 1205 | 98.75 | 0.19727 | 0.19727 | 0.19495 | 0.24059 | RANDOM | 32.446 |
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] | |
1.03 | -0.36 | -0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.068 |
r_dihedral_angle_4_deg | 20.031 |
r_dihedral_angle_3_deg | 16.056 |
r_dihedral_angle_1_deg | 5.567 |
r_scangle_it | 5.276 |
r_scbond_it | 3.881 |
r_mcangle_it | 1.584 |
r_angle_refined_deg | 1.516 |
r_mcbond_it | 1.092 |
r_symmetry_hbond_refined | 0.337 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1980 |
Nucleic Acid Atoms | |
Solvent Atoms | 248 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
HKL-3000 | phasing |