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Structure of factor VII Gla domain bound to EPCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8J experimental model PDB 1DAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.58 65.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 278.406 α = 90 b = 44.222 β = 93.009 c = 111.252 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL DECTRIS EIGER2 XE 9M 2025-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XAIRA 0.97923 ALBA XAIRA
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 3 43.67 93 0.153 0.187 0.106 0.967 4.2 3 25876 48.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 0.48 0.583 0.326 0.705 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 43.67 0.03 25876 1249 88.57 0.2442 0.2416 0.2414 0.2954 0.2968 57.88
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 14.9343 f_angle_d 0.6126 f_chiral_restr 0.0403 f_plane_restr 0.0041 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6407 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 349
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing