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Crystal structure of Nitroreductase from Bacillus tequilensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.2 M Magnesium chloride, 20% PEG3350, MES buffer Ph 6.0
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.472 α = 90 b = 84.279 β = 90 c = 100.606 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.15 46.5 99.6 0.075 0.088 0.044 0.998 10 3.8 157718
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 98.9 0.575 0.679 0.354 0.76 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.15 46.5 149747 7880 99.42 0.12431 0.12304 0.1232 0.14907 0.1498 RANDOM 11.002
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] -1.01 -0.6 1.61
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 28.258 r_mcangle_other 28.252 r_mcbond_it 27.444 r_mcbond_other 27.444 r_long_range_B_refined 17.086 r_scangle_other 16.628 r_long_range_B_other 14.92 r_dihedral_angle_3_deg 11.077 r_dihedral_angle_2_deg 7.406 r_scbond_it 5.778
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 28.258 r_mcangle_other 28.252 r_mcbond_it 27.444 r_mcbond_other 27.444 r_long_range_B_refined 17.086 r_scangle_other 16.628 r_long_range_B_other 14.92 r_dihedral_angle_3_deg 11.077 r_dihedral_angle_2_deg 7.406 r_scbond_it 5.778 r_scbond_other 5.777 r_dihedral_angle_1_deg 5.688 r_rigid_bond_restr 5.218 r_angle_refined_deg 1.811 r_angle_other_deg 0.678 r_chiral_restr 0.109 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3646 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing