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The Crystal Structure of Nitrobenzene Dioxygenase in complex with 3- nitrotoluene
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 MES PH, 6% PEG 8000 (W/V), 5MM NICL2, 50 MM 3-NITROTOLUENE. THE 3-NITROTOLUENE WAS PREPARED FROM A 1M STOCK SOLUTION WHERE 3-NITROTOLUENE HAS BEEN DISOLVED IN ETHANOL.
Crystal Properties Matthews coefficient Solvent content 2.09 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.625 α = 90 b = 121.625 β = 90 c = 84.002 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 2004-02-14 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 1.5 60.86 98.7 0.08 6.7 3.3 108450 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 1.5 1.58 97.6 0.33 3.1 3.3
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 1.5 52.55 105435 5562 98.7 0.17 0.169 0.1678 0.191 0.1886 RANDOM 16.28
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] -0.28 -0.14 -0.28 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.252 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.469 r_scbond_it 1.641 r_angle_refined_deg 1.301 r_mcangle_it 1.052 r_mcbond_it 0.64 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.252 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 6.235 r_scangle_it 2.469 r_scbond_it 1.641 r_angle_refined_deg 1.301 r_mcangle_it 1.052 r_mcbond_it 0.64 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.123 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.09 r_bond_refined_d 0.009 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 5049 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling