1WLI
L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1FLM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | PEG6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.89 | 35 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 36.673 | α = 90 |
b = 79.391 | β = 91.25 |
c = 39.97 | 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 | OXFORD | 2002-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 98 | 29692 | 29692 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.6 | 1.66 | 84.7 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | AB INITIO | THROUGHOUT | 1FLM | 1.6 | 8 | 27871 | 27871 | 1414 | 93.1 | 0.153 | 0.153 | 0.153 | 0.185 | 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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
5 | 2177 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.057 |
s_similar_adp_cmpnt | 0.054 |
s_zero_chiral_vol | 0.045 |
s_from_restr_planes | 0.0274 |
s_angle_d | 0.023 |
s_anti_bump_dis_restr | 0.02 |
s_bond_d | 0.009 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1905 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 62 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHELXL-97 | phasing |