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X-ray structure of soluble EPCR in P212121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 2.8 M sodium acetate pH 8.0, 0.1 M Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.437 α = 90 b = 94.019 β = 90 c = 124.595 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 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.95 41.53 99.9 0.089 0.097 0.038 0.998 10.1 6.5 67837 36.27
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 1.95 2 99.9 1.081 0.447 0.867 1.6 6.8
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 1LQV 1.95 40.32 1.34 67599 3289 99.67 0.201 0.199 0.1985 0.2393 0.2389 RANDOM 45.89
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 12.6849 f_angle_d 1.0773 f_chiral_restr 0.0605 f_plane_restr 0.0103 f_bond_d 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5313 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 549
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing