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Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AZO PDB ENTRY 6AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 1uL 5 mg/mL protein + 1uL 20% w/v PEG3350, 0.2M MgCl2, 20mM Biuret pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.29 α = 90 b = 103.34 β = 90 c = 133.87 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 2.05 81.8 99.7 0.124 8.42 4.25 102760
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 2.05 2.15 99.9 0.425 3.66 4.32
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 6AZO 2.05 56.06 54076 2723 99.9 0.184 0.1932 0.228 0.2323 21.2
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] 1.012 -1.262 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.061 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 6.801 r_angle_refined_deg 1.64 r_angle_other_deg 1.356 r_nbd_refined 0.204 r_nbd_other 0.172 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.061 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 14.114 r_dihedral_angle_1_deg 6.801 r_angle_refined_deg 1.64 r_angle_other_deg 1.356 r_nbd_refined 0.204 r_nbd_other 0.172 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.081 r_gen_planes_other 0.059 r_gen_planes_refined 0.022 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_nbtor_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6856 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building