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Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 MCSG1 screen B10: 24% PEG 4000, 20% glycerol, 160mM MgCl2, 100mM Tris/HCl pH 8.5; BuviA.12245.b.B2.PS02523 at 18.3 mg/ml, + 3mM Alanine; cryo: direct; tray 267436b10, puck LWQ9-7
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.46 α = 90 b = 124.23 β = 101.94 c = 77.04 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-225 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 47.935 99.9 0.092 0.996 12.33 3.8 80654 -3 13.18
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 1.8 1.85 99.9 0.516 2.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4wjb 1.8 47.935 1.35 80600 1959 99.91 0.1393 0.1385 0.1712 0.1595 16.793
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.678 f_angle_d 0.812 f_chiral_restr 0.054 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6166 Nucleic Acid Atoms Solvent Atoms 1026 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction