2ZGZ
PARM with GMPPNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1MWM | PDB CODE 1MWM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | 12% (W/W) PEG 8000, 0.4M SODIUM CHLORID, 0.4M MAGNESIUM ACETATE, 0.1M SODIUM CACODYLATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.9 | 57.55 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 64.214 | α = 90 |
b = 64.214 | β = 90 |
c = 200.913 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 |
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 210 | 2006-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | 1.0000 | SPring-8 | BL44B2 |
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 | 2.25 | 50 | 96.6 | 0.056 | 50.32 | 6.8 | 37157 | 41.2 |
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) | |||||||||||
2.25 | 2.33 | 81.3 | 0.169 | 3.05 | 4 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB CODE 1MWM | 2.25 | 45.41 | 37103 | 1833 | 96.5 | 0.204 | 0.204 | 0.246 | RANDOM | 52.6 |
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] | |
2.97 | 2.97 | -5.94 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.6 |
c_scangle_it | 6.72 |
c_scbond_it | 5.28 |
c_mcangle_it | 4.82 |
c_mcbond_it | 3.49 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.69 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5034 |
Nucleic Acid Atoms | |
Solvent Atoms | 268 |
Heterogen Atoms | 68 |
Software
Software | |
---|---|
Software Name | Purpose |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |