6CZP

2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292Protein: 17.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride, 0.1M Tris pH 8.5, 25% (w/v) PEG3350, Cryo: paratone
Crystal Properties
Matthews coefficientSolvent content
2.3547.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.769α = 90
b = 119.659β = 90
c = 131.175γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.2301000.1290.1290.1380.04838.37.888464-348.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.241000.7680.7680.8260.30.8523.17.3

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 REPLACEMENTTHROUGHOUT1ICR2.2429.9183952443497.580.179620.177330.22392RANDOM49.134
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]
-1.723.56-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.525
r_dihedral_angle_4_deg12.85
r_dihedral_angle_3_deg9.108
r_long_range_B_refined6.633
r_long_range_B_other6.606
r_scangle_other3.343
r_mcangle_it2.458
r_mcangle_other2.458
r_dihedral_angle_1_deg2.165
r_scbond_it2.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg18.525
r_dihedral_angle_4_deg12.85
r_dihedral_angle_3_deg9.108
r_long_range_B_refined6.633
r_long_range_B_other6.606
r_scangle_other3.343
r_mcangle_it2.458
r_mcangle_other2.458
r_dihedral_angle_1_deg2.165
r_scbond_it2.136
r_scbond_other2.136
r_mcbond_it1.592
r_mcbond_other1.592
r_angle_refined_deg1.249
r_angle_other_deg0.438
r_chiral_restr0.052
r_gen_planes_refined0.022
r_gen_planes_other0.019
r_bond_refined_d0.007
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13691
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms320

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing