1PU4

Crystal structure of human vascular adhesion protein-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298potassium/sodium tartrate, imidazole, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.7574.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 225.916α = 90
b = 225.916β = 90
c = 218.668γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8110EMBL/DESY, HAMBURGX11

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
13.22095.90.0213.214.15236726.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.397.20.464613.54588

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KSI3.2205236449745261996.360.218830.218830.216990.25364RANDOM28.543
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]
-3.66-1.83-3.665.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.974
r_scangle_it2.339
r_angle_refined_deg1.771
r_scbond_it1.331
r_angle_other_deg1.086
r_mcangle_it0.961
r_mcbond_it0.499
r_symmetry_vdw_other0.275
r_nbd_other0.236
r_symmetry_vdw_refined0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.974
r_scangle_it2.339
r_angle_refined_deg1.771
r_scbond_it1.331
r_angle_other_deg1.086
r_mcangle_it0.961
r_mcbond_it0.499
r_symmetry_vdw_other0.275
r_nbd_other0.236
r_symmetry_vdw_refined0.228
r_symmetry_hbond_refined0.211
r_nbd_refined0.209
r_xyhbond_nbd_refined0.175
r_nbtor_other0.097
r_chiral_restr0.095
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11063
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
AMoREphasing