1YLR

The structure of E.coli nitroreductase with bound acetate, crystal form 1


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.243.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.58α = 90
b = 57.58β = 90
c = 263.18γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
11.756.2599.90.1073.6849614477531118.8
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)
11.71.7998.80.4031.66.47068

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1ICR1.756.254761247464254099.70.171350.169910.19775RANDOM15.206
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]
-0.7-0.71.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.504
r_dihedral_angle_3_deg11.92
r_dihedral_angle_4_deg10.864
r_dihedral_angle_1_deg5.435
r_scangle_it2.545
r_scbond_it1.751
r_angle_refined_deg1.185
r_mcangle_it0.969
r_mcbond_it0.849
r_angle_other_deg0.777
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.504
r_dihedral_angle_3_deg11.92
r_dihedral_angle_4_deg10.864
r_dihedral_angle_1_deg5.435
r_scangle_it2.545
r_scbond_it1.751
r_angle_refined_deg1.185
r_mcangle_it0.969
r_mcbond_it0.849
r_angle_other_deg0.777
r_symmetry_vdw_other0.332
r_nbd_refined0.205
r_xyhbond_nbd_other0.195
r_mcbond_other0.187
r_nbd_other0.179
r_nbtor_refined0.179
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.145
r_nbtor_other0.083
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3362
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing