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Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 1uL 10mg/mL protein + 1uL 18% w/v PEG3350, 0.2M MgCl2, 1mM triuret pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.1 α = 90 b = 104.4 β = 90 c = 135.3 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 EIGER X 16M 2020-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.991840 APS 23-ID-B
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 1.7 82.66 99.6 0.077 11.55 3.85 186186
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 1.7 1.8 99.9 0.501 2.96 3.77
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6XJM 1.7 56.837 97273 4864 99.858 0.186 0.1844 0.1958 0.2079 0.2153 18.828
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] 0.838 -0.422 -0.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.121 r_dihedral_angle_4_deg 17.882 r_dihedral_angle_3_deg 13.261 r_dihedral_angle_1_deg 5.989 r_lrange_it 4.064 r_lrange_other 4.043 r_scangle_it 3.206 r_scangle_other 3.206 r_scbond_it 2.234 r_scbond_other 2.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.121 r_dihedral_angle_4_deg 17.882 r_dihedral_angle_3_deg 13.261 r_dihedral_angle_1_deg 5.989 r_lrange_it 4.064 r_lrange_other 4.043 r_scangle_it 3.206 r_scangle_other 3.206 r_scbond_it 2.234 r_scbond_other 2.234 r_mcangle_it 2.106 r_mcangle_other 2.106 r_angle_refined_deg 1.647 r_mcbond_it 1.535 r_mcbond_other 1.534 r_angle_other_deg 1.394 r_symmetry_xyhbond_nbd_refined 0.306 r_nbd_refined 0.207 r_symmetry_nbd_other 0.188 r_nbd_other 0.178 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.113 r_symmetry_nbd_refined 0.112 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_5 0.072 r_ncsr_local_group_6 0.071 r_ncsr_local_group_3 0.067 r_ncsr_local_group_4 0.066 r_ncsr_local_group_1 0.065 r_ncsr_local_group_2 0.062 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6856 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing