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The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICU pdb entry 1ICU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.078 α = 90 b = 56.466 β = 103.1 c = 116.085 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2001-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 40 99.6 0.056 8.9 6.5 97110 97110 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 99.5 0.118 5.8 4.6 14083
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1ICU 1.7 40 92255 4855 99.58 0.1449 0.14373 0.1664 0.16685 0.1849 RANDOM 11.066
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] -0.29 0.04 0.29 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.363 r_scangle_it 2.604 r_scbond_it 1.597 r_angle_refined_deg 1.266 r_mcangle_it 0.918 r_angle_other_deg 0.804 r_mcbond_it 0.486 r_nbd_other 0.242 r_symmetry_vdw_other 0.232 r_symmetry_vdw_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.363 r_scangle_it 2.604 r_scbond_it 1.597 r_angle_refined_deg 1.266 r_mcangle_it 0.918 r_angle_other_deg 0.804 r_mcbond_it 0.486 r_nbd_other 0.242 r_symmetry_vdw_other 0.232 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.194 r_xyhbond_nbd_refined 0.161 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6724 Nucleic Acid Atoms Solvent Atoms 902 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing