2VWV

ephB4 kinase domain inhibitor complex


X-RAY DIFFRACTION

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
2.238.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.154α = 90
b = 52.872β = 110.06
c = 57.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU-MSC SATURNMIRRORS2005-02-15MSINGLE 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
11.7310086.20.0511.82.5818158231.59
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)
11.7340.10.41.51.68

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 2VWU1.953.6121815891786.20.2410.2380.287RANDOM36.01
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]
0.8330.487-0.8810.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.181
r_dihedral_angle_4_deg17.555
r_dihedral_angle_3_deg12.641
r_dihedral_angle_1_deg6.669
r_scangle_it2.581
r_scbond_it1.759
r_angle_refined_deg1.437
r_mcangle_it1.243
r_mcbond_it0.713
r_nbd_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.181
r_dihedral_angle_4_deg17.555
r_dihedral_angle_3_deg12.641
r_dihedral_angle_1_deg6.669
r_scangle_it2.581
r_scbond_it1.759
r_angle_refined_deg1.437
r_mcangle_it1.243
r_mcbond_it0.713
r_nbd_refined0.212
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.165
r_chiral_restr0.088
r_symmetry_hbond_refined0.082
r_bond_refined_d0.013
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 Atoms1954
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing