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Factor VII Gla domain, X-ray structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2.0 M Malonate
Crystal Properties Matthews coefficient Solvent content 2.75 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.47 α = 88.335 b = 29.673 β = 78.611 c = 33.259 γ = 76.921
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 EIGER2 XE 9M 2025-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XAIRA 0.97918 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 1.55 32.6 96.8 0.126 0.151 0.083 0.928 3.8 3.3 12546 10.26
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 1.55 1.58 0.521 0.626 0.343 0.832 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 32.6 12546 636 96.806 0.153 0.1519 0.1598 0.1707 0.1772 RANDOM 14.42
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] -0.214 0.859 0.186 -1.158 0.746 1.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.152 r_lrange_it 12.812 r_lrange_other 11.235 r_dihedral_angle_3_deg 9.209 r_dihedral_angle_1_deg 6.778 r_scangle_it 6.266 r_scangle_other 6.259 r_mcangle_it 5.693 r_mcangle_other 5.691 r_scbond_it 4.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.152 r_lrange_it 12.812 r_lrange_other 11.235 r_dihedral_angle_3_deg 9.209 r_dihedral_angle_1_deg 6.778 r_scangle_it 6.266 r_scangle_other 6.259 r_mcangle_it 5.693 r_mcangle_other 5.691 r_scbond_it 4.287 r_scbond_other 4.281 r_mcbond_it 3.857 r_mcbond_other 3.85 r_dihedral_angle_2_deg 3.675 r_rigid_bond_restr 3.639 r_angle_refined_deg 1.772 r_angle_other_deg 0.693 r_symmetry_nbd_refined 0.463 r_nbd_refined 0.281 r_xyhbond_nbd_refined 0.246 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.176 r_nbd_other 0.172 r_symmetry_metal_ion_refined 0.156 r_chiral_restr 0.106 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 557 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing