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Crystal structure of human vascular adhesion protein-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KSI PDB ENTRY 1KSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 potassium/sodium tartrate, imidazole, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.75 74.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.916 α = 90 b = 225.916 β = 90 c = 218.668 γ = 120
Symmetry Space Group P 65 2 2
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 MARRESEARCH 2002-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8110 EMBL/DESY, HAMBURG X11
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 3.2 20 95.9 0.02 13.2 14.1 52367 26.7
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 3.2 3.3 97.2 0.464 6 13.5 4588
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 PDB ENTRY 1KSI 3.2 20 52364 49745 2619 96.36 0.21883 0.21883 0.21699 0.1933 0.25364 0.2293 RANDOM 28.543
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] -3.66 -1.83 -3.66 5.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.974 r_scangle_it 2.339 r_angle_refined_deg 1.771 r_scbond_it 1.331 r_angle_other_deg 1.086 r_mcangle_it 0.961 r_mcbond_it 0.499 r_symmetry_vdw_other 0.275 r_nbd_other 0.236 r_symmetry_vdw_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.974 r_scangle_it 2.339 r_angle_refined_deg 1.771 r_scbond_it 1.331 r_angle_other_deg 1.086 r_mcangle_it 0.961 r_mcbond_it 0.499 r_symmetry_vdw_other 0.275 r_nbd_other 0.236 r_symmetry_vdw_refined 0.228 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.175 r_nbtor_other 0.097 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11063 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data scaling AMoRE phasing