2VWU

ephB4 kinase domain inhibitor complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JPAPDB ENTRY 1JPA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277PROTEIN: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP: 4 DEGREES C SITTING DROP: 2 UL PROTEIN, 0.6 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
2.448.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.49α = 90
b = 53.479β = 111.15
c = 61.392γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2004-11-24MSINGLE 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
11.4556.81000.095.447.119173216.18
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)
122.111000.381.67.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1JPA256.82191599861000.1770.1750.209RANDOM23.29
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]
0.181-0.812-0.343-0.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg17.178
r_dihedral_angle_3_deg11.386
r_dihedral_angle_1_deg5.873
r_scangle_it2.727
r_scbond_it1.749
r_angle_refined_deg1.295
r_mcangle_it1.267
r_mcbond_it0.829
r_nbd_refined0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg17.178
r_dihedral_angle_3_deg11.386
r_dihedral_angle_1_deg5.873
r_scangle_it2.727
r_scbond_it1.749
r_angle_refined_deg1.295
r_mcangle_it1.267
r_mcbond_it0.829
r_nbd_refined0.196
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.149
r_chiral_restr0.082
r_symmetry_hbond_refined0.067
r_symmetry_vdw_refined0.06
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms1958
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing