3BEM

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5277NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.62α = 90
b = 69.2β = 100.54
c = 61.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2007-10-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.91840, 0.97939, 0.97953APS23-ID-D

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
11.6528.583970.0518.9851334-327.797
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)
11.651.7189.90.2912.9

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 DIFFRACTIONMADTHROUGHOUT1.6528.58351310262099.40.1520.1510.175RANDOM17.273
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]
0.34-0.40.09-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.588
r_dihedral_angle_4_deg14.714
r_dihedral_angle_3_deg13.864
r_scangle_it7.211
r_dihedral_angle_1_deg5.984
r_scbond_it5.078
r_mcangle_it3.069
r_mcbond_it2.433
r_angle_refined_deg1.61
r_angle_other_deg0.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.588
r_dihedral_angle_4_deg14.714
r_dihedral_angle_3_deg13.864
r_scangle_it7.211
r_dihedral_angle_1_deg5.984
r_scbond_it5.078
r_mcangle_it3.069
r_mcbond_it2.433
r_angle_refined_deg1.61
r_angle_other_deg0.997
r_mcbond_other0.57
r_symmetry_vdw_refined0.327
r_symmetry_hbond_refined0.246
r_nbd_refined0.228
r_symmetry_vdw_other0.217
r_nbd_other0.2
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.154
r_xyhbond_nbd_other0.107
r_chiral_restr0.094
r_nbtor_other0.088
r_bond_refined_d0.017
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 Atoms3276
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction