4BTW

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
5.0175.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 226.473α = 90
b = 226.473β = 90
c = 219.25γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.850960.323.59.2603291.46
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.8282.65.7

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 1US12.849.3960329317677.860.207810.205040.26032RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.217
r_dihedral_angle_3_deg20.319
r_dihedral_angle_4_deg18.43
r_long_range_B_refined10.426
r_long_range_B_other10.425
r_dihedral_angle_1_deg9.337
r_mcangle_other7.134
r_mcangle_it7.133
r_scangle_other6.874
r_mcbond_it4.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.217
r_dihedral_angle_3_deg20.319
r_dihedral_angle_4_deg18.43
r_long_range_B_refined10.426
r_long_range_B_other10.425
r_dihedral_angle_1_deg9.337
r_mcangle_other7.134
r_mcangle_it7.133
r_scangle_other6.874
r_mcbond_it4.549
r_mcbond_other4.548
r_scbond_it4.336
r_scbond_other4.336
r_angle_refined_deg1.95
r_angle_other_deg0.892
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_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 Atoms106
Heterogen Atoms296

Software

Software
Software NamePurpose
HKLdata reduction
HKLdata scaling
CCP4phasing
MOLREPphasing
REFMACrefinement