4FGC
Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4F8B | PDB ENTRY 4F8B |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.4 | 293.15 | 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, temperature 293.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.5 | 50.79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 93.048 | α = 90 |
b = 93.048 | β = 90 |
c = 193.651 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 200 | CCD | ADSC QUANTUM 315r | mirrors | 2011-02-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 1.000003 | SSRL | BL9-1 |
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 | 2.498 | 22.151 | 91.6 | 0.14 | 6.8 | 4 | 34498 | 31577 | 46.6 |
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 | 2.498 | 2.54 | 88.8 | 0.65 | 2.3 | 3.9 | 1498 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 4F8B | 2.498 | 22.15 | 34397 | 29866 | 1592 | 91.46 | 0.23225 | 0.22836 | 0.30485 | RANDOM | 39.309 |
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] | |
0.36 | 0.18 | 0.36 | -0.54 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.833 |
r_dihedral_angle_4_deg | 11.448 |
r_dihedral_angle_3_deg | 11.073 |
r_scangle_it | 3.033 |
r_dihedral_angle_1_deg | 2.322 |
r_angle_refined_deg | 1.997 |
r_scbond_it | 1.856 |
r_mcangle_it | 1.424 |
r_mcbond_it | 0.744 |
r_chiral_restr | 0.046 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6007 |
Nucleic Acid Atoms | |
Solvent Atoms | 205 |
Heterogen Atoms | 84 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |