2VYQ
FERREDOXIN:NADP REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY, ALA 160 REPLACED BY THR, LEU 263 REPLACED BY PRO AND TYR 303 REPLACED BY SER (T155G-A160T-L263P-Y303S)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1QUE | PDB ENTRY 1QUE |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.5 | 18-20 % (W/V) PEG 6000 20 MM AMMONIUM SULPHATE 0.1M MES/NAOH, PH 5.0-5.5 B-OCTYL GLYCOSIDE AT 2%(W/V) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.85 | 56.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 87.021 | α = 90 |
b = 87.021 | β = 90 |
c = 96.106 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 120 | CCD | BRUKER-NONIUS | 2006-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR |
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 | 1.9 | 75.38 | 99.1 | 0.05 | 23.85 | 5.26 | 30845 | 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) | |||||||||||
1 | 1.9 | 2 | 93.8 | 0.19 | 5.45 | 2.54 |
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 ENTRY 1QUE | 1.9 | 19.8 | 30199 | 2261 | 99.1 | 0.163 | 0.161 | 0.185 | RANDOM | 12.18 |
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 |
r_dihedral_angle_1_deg | 5.263 |
r_scangle_it | 1.94 |
r_scbond_it | 1.11 |
r_angle_refined_deg | 1.023 |
r_mcangle_it | 0.876 |
r_angle_other_deg | 0.724 |
r_mcbond_it | 0.46 |
r_symmetry_vdw_other | 0.252 |
r_symmetry_vdw_refined | 0.246 |
r_nbd_other | 0.227 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2330 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 70 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
MOLREP | phasing |