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Factor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal structure of complex between factor VIII C2 domain and an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D7P PDB ENTRY 1D7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 30.0% PEG 2000, MME 0.15M KBr, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.279 α = 90 b = 58.988 β = 110.65 c = 60.086 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD mirrors 2009-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.04 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 50 93.1 0.084 13.492 3.1 1231 17899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 63.9 0.415 1.6 1231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1D7P 2.07 33.39 15895 15895 840 96.26 0.21966 0.21742 0.26278 0.2438 RANDOM 28.036
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.139 r_dihedral_angle_3_deg 16.427 r_dihedral_angle_4_deg 9.237 r_dihedral_angle_1_deg 7.144 r_scangle_it 3.004 r_scbond_it 2.088 r_angle_refined_deg 1.454 r_mcangle_it 1.425 r_mcbond_it 1.136 r_symmetry_hbond_refined 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.139 r_dihedral_angle_3_deg 16.427 r_dihedral_angle_4_deg 9.237 r_dihedral_angle_1_deg 7.144 r_scangle_it 3.004 r_scbond_it 2.088 r_angle_refined_deg 1.454 r_mcangle_it 1.425 r_mcbond_it 1.136 r_symmetry_hbond_refined 0.353 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2484 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing