1WLI

L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FLM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298PEG6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.673α = 90
b = 79.391β = 91.25
c = 39.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD2002-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XUSPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6982969229692-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6684.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIOTHROUGHOUT1FLM1.682787127871141493.10.1530.1530.1530.185RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
52177
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.057
s_similar_adp_cmpnt0.054
s_zero_chiral_vol0.045
s_from_restr_planes0.0274
s_angle_d0.023
s_anti_bump_dis_restr0.02
s_bond_d0.009
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1905
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms62

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXL-97phasing