4IYM
Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4E4G |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 0.1M MgCl2, 0.1M MES, pH 6.5, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.43 | 49.47 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 159.472 | α = 90 |
b = 170.91 | β = 106.33 |
c = 170.466 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
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 | 2012-10-16 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
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 | 2.2 | 50 | 99.8 | 0.131 | 5.6 | 3.8 | 440045 |
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 | 2.2 | 2.24 | 99.3 | 0.64 | 3.7 | 21797 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4E4G | 2.2 | 19.99 | 439434 | 22028 | 99.48 | 0.1673 | 0.1651 | 0.16 | 0.2094 | 0.21 | RANDOM | 26.892 |
Anisotropic B[1][3] | Anisotropic B[2][2] |
---|---|
-0.01 | 0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.714 |
r_dihedral_angle_4_deg | 17.498 |
r_dihedral_angle_3_deg | 14.586 |
r_dihedral_angle_1_deg | 5.832 |
r_angle_refined_deg | 1.309 |
r_chiral_restr | 0.089 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 58959 |
Nucleic Acid Atoms | |
Solvent Atoms | 4622 |
Heterogen Atoms | 710 |
Software
Software | |
---|---|
Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
HKL-3000 | data reduction |