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Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1US1 PDB ENTRY 1US1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.6-0.75 M NA/K TARTRATE, 0.2 M NACL, 0.1 M HEPES PH 7.4-7.6
Crystal Properties Matthews coefficient Solvent content 5.03 75.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.736 α = 90 b = 226.736 β = 90 c = 218.16 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 2011-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 3.1 50 98.7 0.29 4.9 4.3 43449 1.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 92.5 3
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 1US1 3.1 49.2 43449 2314 76.19 0.18728 0.1842 0.2148 0.24638 0.2691 RANDOM
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] -0.49 -0.49 -0.49 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_3_deg 20.266 r_dihedral_angle_4_deg 19.073 r_long_range_B_refined 13.991 r_long_range_B_other 13.991 r_dihedral_angle_1_deg 9.52 r_scangle_other 9.388 r_mcangle_it 8.451 r_mcangle_other 8.45 r_scbond_it 6.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_3_deg 20.266 r_dihedral_angle_4_deg 19.073 r_long_range_B_refined 13.991 r_long_range_B_other 13.991 r_dihedral_angle_1_deg 9.52 r_scangle_other 9.388 r_mcangle_it 8.451 r_mcangle_other 8.45 r_scbond_it 6.084 r_scbond_other 6.083 r_mcbond_it 5.482 r_mcbond_other 5.481 r_angle_refined_deg 2.629 r_angle_other_deg 0.918 r_chiral_restr 0.148 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11171 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 273
Software Software Software Name Purpose HKL data reduction HKL data scaling CCP4 phasing MOLREP phasing REFMAC refinement