2VWW

ephB4 kinase domain inhibitor complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VWUPDB ENTRY 2VWU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291CRYSTALLIZATION CONDITIONS: PROTEIN\: 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\:18 DEGREES C SITTING DROP\: 2 UL PROTEIN, 0.6 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
2.344

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.462α = 90
b = 53.414β = 111.38
c = 61.644γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU-MSC SATURNMIRRORS2005-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.917.2195.50.0610.742.1317968220.68
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)
11.91.9293.60.381.993.6

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 2VWU1.919.321796791880.50.1860.1840.229RANDOM30.52
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_deg36.73
r_dihedral_angle_4_deg20.922
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg6.025
r_scangle_it2.91
r_scbond_it1.922
r_angle_refined_deg1.351
r_mcangle_it1.229
r_mcbond_it0.867
r_nbd_refined0.213
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.73
r_dihedral_angle_4_deg20.922
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg6.025
r_scangle_it2.91
r_scbond_it1.922
r_angle_refined_deg1.351
r_mcangle_it1.229
r_mcbond_it0.867
r_nbd_refined0.213
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.155
r_chiral_restr0.081
r_bond_refined_d0.012
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 Atoms1970
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing