3GIR
Crystal structure of glycine cleavage system aminomethyltransferase T from Bartonella henselae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | PROPLEX SCREEN, H4: 1.4M NA MALONATE, BAHEA.00657.A AT 44.8 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.21 | 61.73 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 54.98 | α = 90 |
b = 72.67 | β = 90 |
c = 138.02 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | ADSC QUANTUM 315 | 2009-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | ALS | 5.0.3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.6 | 69.01 | 95.3 | 0.044 | 0.044 | 16.45 | 3.5 | 70368 | 70368 | -3 | 26.43 |
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) | |||||||||||
1.6 | 1.64 | 98.9 | 0.493 | 2.6 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MR, MR | THROUGHOUT | pdb entry 1wsr, modified with ccp4 program chainsaw | 1.6 | 69.01 | 70311 | 70311 | 3550 | 95.3 | 0.176 | 0.175 | 0.205 | RANDOM | 17.91 |
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] | |
0.85 | -0.2 | -0.65 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.965 |
r_dihedral_angle_4_deg | 16.238 |
r_dihedral_angle_3_deg | 12.325 |
r_dihedral_angle_1_deg | 6.221 |
r_scangle_it | 5.436 |
r_scbond_it | 3.228 |
r_mcangle_it | 2.136 |
r_angle_refined_deg | 1.845 |
r_mcbond_it | 1.236 |
r_angle_other_deg | 1.02 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2823 |
Nucleic Acid Atoms | |
Solvent Atoms | 531 |
Heterogen Atoms | 1 |
Software
Software | |
---|---|
Software Name | Purpose |
BOS | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |