☰ Navigation Tabs
ephB4 kinase domain inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPA PDB ENTRY 1JPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 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: 4 DEGREES C SITTING DROP: 2 UL PROTEIN, 0.6 UL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 2.4 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.49 α = 90 b = 53.479 β = 111.15 c = 61.392 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 ADSC CCD MIRRORS 2004-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.45 56.8 100 0.09 5.44 7.1 19173 2 16.18
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 2.11 100 0.38 1.6 7.15
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 1JPA 2 56.8 2 19159 986 100 0.177 0.175 0.2053 0.209 0.2431 RANDOM 23.29
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] 0.181 -0.812 -0.343 -0.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.975 r_dihedral_angle_4_deg 17.178 r_dihedral_angle_3_deg 11.386 r_dihedral_angle_1_deg 5.873 r_scangle_it 2.727 r_scbond_it 1.749 r_angle_refined_deg 1.295 r_mcangle_it 1.267 r_mcbond_it 0.829 r_nbd_refined 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.975 r_dihedral_angle_4_deg 17.178 r_dihedral_angle_3_deg 11.386 r_dihedral_angle_1_deg 5.873 r_scangle_it 2.727 r_scbond_it 1.749 r_angle_refined_deg 1.295 r_mcangle_it 1.267 r_mcbond_it 0.829 r_nbd_refined 0.196 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.067 r_symmetry_vdw_refined 0.06 r_bond_refined_d 0.011 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 1958 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing