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SAM domain of human ephrin type-a receptor 7 (EPHA7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.1 WELL SOLUTION: 20% PEG 4000, 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K
Crystal Properties Matthews coefficient Solvent content 2.043553 39.810699
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.071 α = 90 b = 54.089 β = 104.84 c = 40.455 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 IMAGE PLATE RIGAKU RAXIS IV 2009-04-03 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 2.1 22.24 97.4 0.05 25.4 3.2 9717 9717 -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) 2.1 2.18 81.1 0.315 2.59 2.2
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 1B4F 2.1 22.24 9717 9162 458 97.73 0.19867 0.19708 0.22767 0.2355 RANDOM 20.025
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] 0.13 -1.49 -1.82 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 4.632 r_scangle_it 3.137 r_scbond_it 1.946 r_angle_refined_deg 1.245 r_mcangle_it 0.989 r_mcbond_it 0.492 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.899 r_dihedral_angle_4_deg 19.234 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 4.632 r_scangle_it 3.137 r_scbond_it 1.946 r_angle_refined_deg 1.245 r_mcangle_it 0.989 r_mcbond_it 0.492 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1174 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling