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The Crystal Structure of Nitrobenzene Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7W PDB ENTRY 1O7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M MES PH 6.0, 6% PEG 8000 (W/V), 5MM NICL2
Crystal Properties Matthews coefficient Solvent content 2.06 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.586 α = 90 b = 121.586 β = 90 c = 84.356 γ = 120
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 CCD MIRRORS 2003-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.2 52 95 0.09 4.1 6.5 207117 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.26 91.8 0.61 1.4 4.5
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 1O7W 1.2 52 198985 10509 95 0.156 0.156 0.1561 0.172 0.1726 RANDOM 16.1
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] -0.37 -0.19 -0.37 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 14.192 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 6.338 r_scangle_it 2.318 r_scbond_it 1.91 r_angle_refined_deg 1.27 r_mcangle_it 1.266 r_mcbond_it 0.826 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 14.192 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 6.338 r_scangle_it 2.318 r_scbond_it 1.91 r_angle_refined_deg 1.27 r_mcangle_it 1.266 r_mcbond_it 0.826 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.1 r_symmetry_hbond_refined 0.09 r_chiral_restr 0.087 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5049 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing