4BTY

Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1US1PDB ENTRY 1US1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.6-0.75 M NA/K TARTRATE, 0.2 M NACL, 0.1 M HEPES PH 7.4-7.6
Crystal Properties
Matthews coefficientSolvent content
5.0375.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 226.736α = 90
b = 226.736β = 90
c = 218.16γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2011-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.15098.70.294.94.3434491.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.1592.53

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1US13.149.243449231476.190.187280.18420.24638RANDOM
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]
-0.49-0.49-0.491.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.536
r_dihedral_angle_3_deg20.266
r_dihedral_angle_4_deg19.073
r_long_range_B_refined13.991
r_long_range_B_other13.991
r_dihedral_angle_1_deg9.52
r_scangle_other9.388
r_mcangle_it8.451
r_mcangle_other8.45
r_scbond_it6.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.536
r_dihedral_angle_3_deg20.266
r_dihedral_angle_4_deg19.073
r_long_range_B_refined13.991
r_long_range_B_other13.991
r_dihedral_angle_1_deg9.52
r_scangle_other9.388
r_mcangle_it8.451
r_mcangle_other8.45
r_scbond_it6.084
r_scbond_other6.083
r_mcbond_it5.482
r_mcbond_other5.481
r_angle_refined_deg2.629
r_angle_other_deg0.918
r_chiral_restr0.148
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms11171
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms273

Software

Software
Software NamePurpose
HKLdata reduction
HKLdata scaling
CCP4phasing
MOLREPphasing
REFMACrefinement