4BTX

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
4.9174.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 226.35α = 90
b = 226.35β = 90
c = 217.226γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-05-05MSINGLE 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
12.785099.90.1819.47629172.36
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.782.8399.55.4

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 1US12.7849.0562917331980.410.183460.180650.23679RANDOM39.991
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]
0.660.660.66-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg20.278
r_dihedral_angle_3_deg19.573
r_dihedral_angle_1_deg8.616
r_mcangle_it4.403
r_scbond_it2.714
r_mcbond_it2.63
r_mcbond_other2.621
r_angle_refined_deg1.73
r_angle_other_deg0.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg20.278
r_dihedral_angle_3_deg19.573
r_dihedral_angle_1_deg8.616
r_mcangle_it4.403
r_scbond_it2.714
r_mcbond_it2.63
r_mcbond_other2.621
r_angle_refined_deg1.73
r_angle_other_deg0.858
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 AtomsNumber
Protein Atoms11156
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms238

Software

Software
Software NamePurpose
HKLdata reduction
HKLdata scaling
CCP4phasing
MOLREPphasing
REFMACrefinement