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The structure of E. coli nitroreductase with bound acetate, crystal form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICV pdb entry 1ICV
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 36.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.661 α = 90 b = 46.94 β = 90 c = 53.658 γ = 90
Symmetry Space Group P 21 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 2000-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97626 ESRF BM14
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 2 26.93 95.6 0.071 13.1 3 26207 26207 1 1 15.9
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) 2 2.11 95.7 0.173 5.4 2.6 3743
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 1ICV 2 53.45 24904 1302 95.53 0.1467 0.14384 0.1497 0.20312 0.2061 RANDOM 10.381
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] -0.84 2 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.498 r_scangle_it 2.376 r_scbond_it 1.428 r_angle_refined_deg 1.077 r_mcangle_it 0.784 r_angle_other_deg 0.752 r_mcbond_it 0.409 r_nbd_other 0.236 r_symmetry_vdw_other 0.21 r_symmetry_hbond_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.498 r_scangle_it 2.376 r_scbond_it 1.428 r_angle_refined_deg 1.077 r_mcangle_it 0.784 r_angle_other_deg 0.752 r_mcbond_it 0.409 r_nbd_other 0.236 r_symmetry_vdw_other 0.21 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.164 r_nbtor_other 0.083 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 3354 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing