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High resolution crystal structure of the MCR-2 catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Reservoir: 0.1 M KSCN, 30% PEG2000MME;
Protein: 15 mg/ml, 50 mM HEPES pH7.5, 150 mM NaCl, 0.1mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 1.95 36.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.818 α = 90 b = 53.31 β = 90 c = 117.509 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 PILATUS 6M-F 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.12 58.75 99.8 0.017 1 20.4 11.7 108679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.14 96.8 0.192 0.879 3.4 6.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LRN 1.12 48.548 1.35 108679 5480 99.77 0.134 0.1334 0.1351 0.1453 0.1457
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 13.457 f_angle_d 1.382 f_chiral_restr 0.083 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2537 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing