2ODO
Crystal structure of Pseudomonas Fluorescens alanine racemase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | VAPOR DIFFUSION, HANGING DROP | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.87 | 57.19 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 186.739 | α = 90 |
| b = 186.739 | β = 90 |
| c = 103.657 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 41 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS V | mirrors | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
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 | 2.8 | 50 | 93.7 | 0.085 | 5.4 | 3.5 | 41244 | 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) | |||||||||||
| 1 | 2.8 | 2.9 | 61.4 | 0.318 | 1.9 | 2683 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | 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 | 1RCQ | 2.8 | 46.32 | 1 | 41244 | 39114 | 2076 | 93.53 | 0.2159 | 0.21431 | 0.24659 | RANDOM | 53.213 | ||||
| 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] | |
| -0.14 | -0.14 | 0.29 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.168 |
| r_dihedral_angle_4_deg | 16.084 |
| r_dihedral_angle_3_deg | 14.926 |
| r_dihedral_angle_1_deg | 4.877 |
| r_angle_refined_deg | 1.046 |
| r_scangle_it | 0.476 |
| r_mcangle_it | 0.36 |
| r_nbtor_refined | 0.293 |
| r_scbond_it | 0.262 |
| r_symmetry_hbond_refined | 0.251 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11000 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 58 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
