2ZJB
Crystal structure of the human Dmc1-M200V polymorphic variant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1V5W | PDB ENTRY 1V5W |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.8 | 293 | 0.1M sodium citrate, 50mM MgCl2, 8% PEG 2000 MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.76 | 55.44 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 124.089 | α = 90 |
b = 124.089 | β = 90 |
c = 217.87 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 4 2 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 | MAR CCD 225 mm | 2007-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 1.0 | SPring-8 | BL26B2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.5 | 50 | 100 | 0.085 | 33.1 | 13.1 | 11303 | 11293 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
3.5 | 3.63 | 100 | 0.464 | 6 | 13.8 | 1096 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1V5W | 3.5 | 20 | 11035 | 11034 | 1138 | 0.294 | 0.351 | RANDOM |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.8 |
c_angle_d | 1.32 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3748 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |