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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 CRYSTALLIZATION 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 coefficient Solvent content 2.3 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.462 α = 90 b = 53.414 β = 111.38 c = 61.644 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 SATURN MIRRORS 2005-06-10 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 1.9 17.21 95.5 0.06 10.74 2.13 17968 2 20.68
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 1.9 1.92 93.6 0.38 1.9 93.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.9 19.3 2 17967 918 80.5 0.186 0.184 0.2112 0.229 0.2521 RANDOM 30.52
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 20.922 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.025 r_scangle_it 2.91 r_scbond_it 1.922 r_angle_refined_deg 1.351 r_mcangle_it 1.229 r_mcbond_it 0.867 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.73 r_dihedral_angle_4_deg 20.922 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.025 r_scangle_it 2.91 r_scbond_it 1.922 r_angle_refined_deg 1.351 r_mcangle_it 1.229 r_mcbond_it 0.867 r_nbd_refined 0.213 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 1970 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing