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The structure of E.coli nitroreductase with bound acetate, crystal form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICR pdb entry 1ICR
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 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.58 α = 90 b = 57.58 β = 90 c = 263.18 γ = 90
Symmetry Space Group P 41 21 2
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 2000-09-19 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 56.25 99.9 0.107 3.6 8 49614 47753 1 1 18.8
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 1.7 1.79 98.8 0.403 1.6 6.4 7068
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ICR 1.7 56.25 47612 47464 2540 99.7 0.17135 0.16991 0.1806 0.19775 0.2049 RANDOM 15.206
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 -0.7 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_3_deg 11.92 r_dihedral_angle_4_deg 10.864 r_dihedral_angle_1_deg 5.435 r_scangle_it 2.545 r_scbond_it 1.751 r_angle_refined_deg 1.185 r_mcangle_it 0.969 r_mcbond_it 0.849 r_angle_other_deg 0.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_3_deg 11.92 r_dihedral_angle_4_deg 10.864 r_dihedral_angle_1_deg 5.435 r_scangle_it 2.545 r_scbond_it 1.751 r_angle_refined_deg 1.185 r_mcangle_it 0.969 r_mcbond_it 0.849 r_angle_other_deg 0.777 r_symmetry_vdw_other 0.332 r_nbd_refined 0.205 r_xyhbond_nbd_other 0.195 r_mcbond_other 0.187 r_nbd_other 0.179 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.145 r_nbtor_other 0.083 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3362 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing