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Crystal structure of human factor VIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SDD homology models of individual domain built by SWISS-MODEL using PDB entries 1SDD, 1KCW and 1D7P. experimental model PDB 1KCW homology models of individual domain built by SWISS-MODEL using PDB entries 1SDD, 1KCW and 1D7P. experimental model PDB 1D7P homology models of individual domain built by SWISS-MODEL using PDB entries 1SDD, 1KCW and 1D7P.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 100 mM Tris-HCl, 10% EtOH, 7% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.75 74.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.113 α = 90 b = 134.113 β = 90 c = 349.76 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 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) 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 3.98 50 99 0.13 27.2 13.2 26444 1 1
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 3.98 92.3 0.827 1.7 8.9
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 homology models of individual domain built by SWISS-MODEL using PDB entries 1SDD, 1KCW and 1D7P. 3.98 50 26444 1399 98.55 0.259 0.256 0.2506 0.327 0.3181 RANDOM 199.234
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] 4.46 4.46 -8.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_3_deg 24.514 r_dihedral_angle_4_deg 18.451 r_dihedral_angle_1_deg 9.793 r_angle_refined_deg 1.735 r_scangle_it 1.208 r_mcangle_it 0.751 r_scbond_it 0.712 r_mcbond_it 0.415 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_3_deg 24.514 r_dihedral_angle_4_deg 18.451 r_dihedral_angle_1_deg 9.793 r_angle_refined_deg 1.735 r_scangle_it 1.208 r_mcangle_it 0.751 r_scbond_it 0.712 r_mcbond_it 0.415 r_nbtor_refined 0.322 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.201 r_chiral_restr 0.123 r_symmetry_hbond_refined 0.121 r_metal_ion_refined 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10211 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 106
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling