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Nitrophenol monooxygenase RsPNPA from Rhodococcus sp. 21391
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.056 M NaH2PO4, 1.344 M K2HPO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.561 α = 90 b = 149.561 β = 90 c = 322.141 γ = 90
Symmetry Space Group I 41 2 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 PIXEL DECTRIS PILATUS3 S 6M 2018-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000000 Photon Factory BL-17A
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 2.4 49.32 99.8 0.077 0.08 0.022 1 21.2 13.4 71504
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 2.4 2.45 99.1 1.141 1.185 0.317 0.923 13.7
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 SAD THROUGHOUT 2.4 49.27 67885 3620 99.84 0.23006 0.22727 0.2323 0.28188 0.2866 RANDOM 56.615
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] 0.79 0.79 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.993 r_long_range_B_other 9.012 r_long_range_B_refined 9.006 r_dihedral_angle_2_deg 8.28 r_scangle_other 7.195 r_dihedral_angle_1_deg 6.67 r_mcangle_other 6.22 r_mcangle_it 6.219 r_scbond_it 4.931 r_scbond_other 4.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.993 r_long_range_B_other 9.012 r_long_range_B_refined 9.006 r_dihedral_angle_2_deg 8.28 r_scangle_other 7.195 r_dihedral_angle_1_deg 6.67 r_mcangle_other 6.22 r_mcangle_it 6.219 r_scbond_it 4.931 r_scbond_other 4.931 r_mcbond_it 4.484 r_mcbond_other 4.477 r_angle_refined_deg 1.551 r_angle_other_deg 0.56 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11719 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing