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ephB4 kinase domain inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VWU PDB ENTRY 2VWU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 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 coefficient Solvent content 2.08 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.116 α = 90 b = 53.537 β = 110.9 c = 61.505 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU-MSC MIRRORS 2005-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 100 85.2 0.07 10.1 3.3 28794 2 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 27.5 0.36 2 1.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VWU 1.65 57.45 27330 1464 85.17 0.17267 0.17069 0.1902 0.2102 0.2325 RANDOM 19.122
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] -0.23 -0.53 -0.12 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_4_deg 14.609 r_dihedral_angle_3_deg 12.041 r_dihedral_angle_1_deg 5.485 r_scangle_it 3.149 r_scbond_it 2.17 r_angle_refined_deg 1.469 r_mcangle_it 1.348 r_mcbond_it 0.972 r_angle_other_deg 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_4_deg 14.609 r_dihedral_angle_3_deg 12.041 r_dihedral_angle_1_deg 5.485 r_scangle_it 3.149 r_scbond_it 2.17 r_angle_refined_deg 1.469 r_mcangle_it 1.348 r_mcbond_it 0.972 r_angle_other_deg 0.812 r_symmetry_vdw_other 0.259 r_nbd_refined 0.215 r_nbtor_refined 0.186 r_nbd_other 0.177 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_refined 0.091 r_chiral_restr 0.088 r_nbtor_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 Atoms Number Protein Atoms 2123 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing