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Crystal Structure of the K. lactis Urea Amidolyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VA7 3VA7, 4ISS experimental model PDB 4ISS 3VA7, 4ISS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 0.1M Tris/HCl (pH 7.5), 0.2M ammonium sulfate, 12% PEG 8000, 2% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.27 62.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.74 α = 90 b = 181.94 β = 90 c = 549.82 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 CCD ADSC QUANTUM 315 2015-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 6.5 274.91 95.6 0.118 0.137 0.066 8.3 3.9 20690 20690 219.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 6.5 6.85 97.1 0.581 0.581 0.671 0.324 1.3 4 2984
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 3VA7, 4ISS 6.5 29.98 1.34 20603 1015 95.77 0.2789 0.2776 0.2737 0.3022 0.3009 Random 308.3873
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 17.885 f_angle_d 1.638 f_chiral_restr 0.078 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51722 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data collection SCALA data scaling PHASER phasing PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing