3VY5

N33Q mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527720% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 16.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.3748.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.767α = 90
b = 83.993β = 93.74
c = 40.445γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2011-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.4201000.0597.448156
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.481000.2797.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FLM1.42045694243499.980.166940.166040.18397RANDOM15.91
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]
-0.88-0.050.480.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.108
r_dihedral_angle_4_deg10.978
r_dihedral_angle_3_deg10.665
r_dihedral_angle_1_deg5.839
r_scangle_it2.781
r_scbond_it1.722
r_angle_refined_deg1.165
r_mcangle_it1.109
r_mcbond_it0.59
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.108
r_dihedral_angle_4_deg10.978
r_dihedral_angle_3_deg10.665
r_dihedral_angle_1_deg5.839
r_scangle_it2.781
r_scbond_it1.722
r_angle_refined_deg1.165
r_mcangle_it1.109
r_mcbond_it0.59
r_chiral_restr0.083
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1854
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms63

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling