1YLU

The structure of E. coli nitroreductase with bound acetate, crystal form 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICVpdb entry 1ICV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6291PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
236.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.661α = 90
b = 46.94β = 90
c = 53.658γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97626ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1226.9395.60.07113.1326207262071115.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1195.70.1735.42.63743

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 1ICV253.4524904130295.530.14670.143840.20312RANDOM10.381
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]
-0.842-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.498
r_scangle_it2.376
r_scbond_it1.428
r_angle_refined_deg1.077
r_mcangle_it0.784
r_angle_other_deg0.752
r_mcbond_it0.409
r_nbd_other0.236
r_symmetry_vdw_other0.21
r_symmetry_hbond_refined0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.498
r_scangle_it2.376
r_scbond_it1.428
r_angle_refined_deg1.077
r_mcangle_it0.784
r_angle_other_deg0.752
r_mcbond_it0.409
r_nbd_other0.236
r_symmetry_vdw_other0.21
r_symmetry_hbond_refined0.204
r_nbd_refined0.197
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.164
r_nbtor_other0.083
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3354
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing