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Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JB9 5JB9, 5VYG experimental model PDB 5VYG 5JB9, 5VYG
Crystallization Crystalization Experiments ID Method pH Temperature Details dg9lite_soak1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.247 α = 90 b = 90.247 β = 90 c = 156.347 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 dg9lite_soak1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 4 1.88 78.16 99.3 0.095 0.104 0.042 0.997 11.1 6 52703 24.65
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) 4 1.88 1.92 99 0.678 0.74 0.292 0.854 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5JB9, 5VYG 1.88 78.16 49995 2660 98.86 0.1855 0.1842 0.1947 0.2112 0.2217 RANDOM 30.374
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] -0.82 -0.82 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 13.957 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.672 r_angle_refined_deg 1.392 r_angle_other_deg 1.099 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 13.957 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.672 r_angle_refined_deg 1.392 r_angle_other_deg 1.099 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5058 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction