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PCE reductive dehalogenase from S. multivorans with 6-hydroxybenzimidazolyl norcobamide cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 15 percent PEG 3350, 200 mM sodium malonate, 2 percent benzamidineHCl, and 50 mM TrisHCl, pH 7.5 under an atmosphere of 95 percent N2, 5 percent H2 and less than 10 ppm oxygen
Crystal Properties Matthews coefficient Solvent content 2.5 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.565 α = 90 b = 73.565 β = 90 c = 184.677 γ = 90
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 PILATUS 6M-F 2016-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.91841 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.593 36.074 99.33 0.1139 0.0325 0.999 14.92 13.2 129361 2 18.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.593 1.65 93.44 0.9312 0.2697 0.802 1.92 12.6
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 4UQU 1.593 36.074 1.29 129111 6455 99.25 0.1536 0.1524 0.154 0.1766 0.1781 Random Selection
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 3.881 f_angle_d 0.93 f_chiral_restr 0.059 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6796 Nucleic Acid Atoms Solvent Atoms 864 Heterogen Atoms 243
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing