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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 2.8M sodium chloride, 0.1M Tris-HCl, 3% glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.168 α = 90 b = 55.492 β = 90 c = 68.336 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 CCD MARMOSAIC 325 mm CCD mirrors 2008-03-30 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 1.07 50 97.7 0.065 29.044 5.7 6479 69391
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) 1.07 1.11 92.5 0.349 29.05 3.1 6479
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 (All) 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 1D7P 1.07 21.95 46406 46406 2342 65.27 0.199 0.184 0.183 0.1784 0.201 0.195 RANDOM 9.742
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] -0.03 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.25 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_4_deg 11.612 r_dihedral_angle_1_deg 6.559 r_sphericity_free 5.176 r_sphericity_bonded 3.657 r_scangle_it 2.93 r_scbond_it 2.193 r_mcangle_it 1.627 r_angle_refined_deg 1.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.25 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_4_deg 11.612 r_dihedral_angle_1_deg 6.559 r_sphericity_free 5.176 r_sphericity_bonded 3.657 r_scangle_it 2.93 r_scbond_it 2.193 r_mcangle_it 1.627 r_angle_refined_deg 1.418 r_rigid_bond_restr 1.181 r_mcbond_it 1.165 r_nbtor_refined 0.303 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.096 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1242 Nucleic Acid Atoms Solvent Atoms 119 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