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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 1PU4 PDB ENTRY 1PU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.00
Crystal Properties Matthews coefficient Solvent content 4.6 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.099 α = 90 b = 226.099 β = 90 c = 223.004 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 2003-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.9 20 93.3 0.121 19 10.4 69536
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 2.9 3 95.3 0.474 6.4 10.4
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 PDB ENTRY 1PU4 2.9 19.96 69536 3476 93.3 0.242 0.241 0.2238 0.267 0.2469 RANDOM 41.04
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] -5.68 -2.84 -5.68 8.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.822 r_scangle_it 2.705 r_angle_refined_deg 1.891 r_scbond_it 1.571 r_mcangle_it 1.041 r_angle_other_deg 0.99 r_mcbond_it 0.539 r_symmetry_vdw_refined 0.339 r_nbd_other 0.234 r_symmetry_vdw_other 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.822 r_scangle_it 2.705 r_angle_refined_deg 1.891 r_scbond_it 1.571 r_mcangle_it 1.041 r_angle_other_deg 0.99 r_mcbond_it 0.539 r_symmetry_vdw_refined 0.339 r_nbd_other 0.234 r_symmetry_vdw_other 0.228 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.1 r_nbtor_other 0.094 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_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 reduction XDS data scaling