3GFA

Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.727743.1000% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5952.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.336α = 90
b = 109.891β = 104.84
c = 60.635γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-11-14MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91162,0.97831,0.97870SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.3529.98898.20.0820.0823.9383.79964914.166
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3981.90.4960.4961.536124

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.3529.98899648498398.220.1350.1340.157RANDOM18.461
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]
-0.4-0.96-0.380.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.42
r_dihedral_angle_4_deg13.771
r_dihedral_angle_3_deg12.78
r_sphericity_free7.409
r_dihedral_angle_1_deg5.547
r_sphericity_bonded3.701
r_scangle_it2.876
r_mcangle_it2.61
r_scbond_it2.093
r_mcbond_it1.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.42
r_dihedral_angle_4_deg13.771
r_dihedral_angle_3_deg12.78
r_sphericity_free7.409
r_dihedral_angle_1_deg5.547
r_sphericity_bonded3.701
r_scangle_it2.876
r_mcangle_it2.61
r_scbond_it2.093
r_mcbond_it1.932
r_angle_refined_deg1.504
r_rigid_bond_restr1.335
r_mcbond_other1.026
r_angle_other_deg0.941
r_symmetry_vdw_refined0.267
r_symmetry_vdw_other0.225
r_nbd_refined0.223
r_symmetry_hbond_refined0.205
r_nbd_other0.201
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.15
r_nbtor_other0.089
r_chiral_restr0.086
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3077
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction