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Complex between the kinase domain of human ephrin type-a receptor 7 (epha7) and inhibitor alw-ii-49-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2REI PDB ENTRY 2REI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO WHICH MPD WAS ADDED TO 25%, , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.658 α = 90 b = 52.658 β = 90 c = 217.059 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 25 95.4 0.067 38.92 9.9 21903 21903 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 98.1 0.417 4.19 6.5 2253
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2REI 2 23.69 21809 20747 1062 95.3 0.19118 0.18917 0.2316 0.2239 RANDOM 27.811
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] 1.06 0.53 1.06 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.222 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_1_deg 5.13 r_scangle_it 2.329 r_scbond_it 1.451 r_angle_refined_deg 1.156 r_mcangle_it 0.939 r_mcbond_it 0.599 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.222 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_1_deg 5.13 r_scangle_it 2.329 r_scbond_it 1.451 r_angle_refined_deg 1.156 r_mcangle_it 0.939 r_mcbond_it 0.599 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 30
Software Software Software Name Purpose PHASER phasing REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling