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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 2.14 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.123 α = 90 b = 53.492 β = 110.91 c = 61.265 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 2.1 100 100 0.13 5.6 3.66 16426 2
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 2.1 2.18 100 0.31 2.8 3.6
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 2.1 57.26 15595 831 99.95 0.18681 0.18436 0.199 0.23286 0.2438 RANDOM 22.306
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] 0.35 -0.58 -1.07 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 15.006 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 5.953 r_scangle_it 2.785 r_scbond_it 1.863 r_angle_refined_deg 1.461 r_mcangle_it 1.258 r_mcbond_it 0.872 r_angle_other_deg 0.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 15.006 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 5.953 r_scangle_it 2.785 r_scbond_it 1.863 r_angle_refined_deg 1.461 r_mcangle_it 1.258 r_mcbond_it 0.872 r_angle_other_deg 0.819 r_symmetry_vdw_other 0.246 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.218 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.177 r_symmetry_vdw_refined 0.115 r_chiral_restr 0.088 r_nbtor_other 0.081 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 2109 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing