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Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia multivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I4M PDB entry 5I4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 RigakuReagents JCSG+ screen, B2: 25% PEG 3350, 200mM Sodium thiocyanate; BumuA.12245.e.B1.PW37879 at 19.5mg/ml; cryo: 20% EG; tray 272537b2, puck ujd4-3
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.46 α = 90 b = 88.51 β = 90.21 c = 126.44 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-300 2016-06-08 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 2.5 50 98.6 0.08 0.997 14.21 3.86 65364 -3 37.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 98.2 0.494 0.82 2.89
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5I4M 2.5 39.394 1.36 65358 2083 98.66 0.1564 0.1546 0.1571 0.2122 0.2146 0 45.0811
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 17.46 f_angle_d 0.735 f_chiral_restr 0.051 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12302 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 32
Software Software Software Name Purpose XDS data scaling XSCALE data scaling MOLREP phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction