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The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMO PDB ENTRY 2BMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M HEPES PH 6.5, 6% PEG 8000 (W/V), 5MM NISO4, 50 MM NITROBENZENE. THE NITROBENZENE WAS PREPARED FROM A 1M STOCKSOLUTION WHERE NITROBENZENE WAS DISOLVED IN ETHANOL.
Crystal Properties Matthews coefficient Solvent content 2.15 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.533 α = 90 b = 121.533 β = 90 c = 84.179 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 MARRESEARCH 2003-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.55 27.63 98.5 0.08 6.7 5.1 99964 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 1.55 1.63 99.7 0.51 1.4 4.3
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 2BMO 1.55 27 95726 5050 98.5 0.169 0.167 0.1669 0.192 0.1913 RANDOM 17.71
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] -0.44 -0.22 -0.44 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 17.613 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 6.234 r_scangle_it 2.55 r_scbond_it 1.779 r_angle_refined_deg 1.306 r_mcangle_it 1.095 r_mcbond_it 0.658 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 17.613 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 6.234 r_scangle_it 2.55 r_scbond_it 1.779 r_angle_refined_deg 1.306 r_mcangle_it 1.095 r_mcbond_it 0.658 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 5048 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling