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Human EphA3 kinase domain, base structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSF PDB entry 2GSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.59 α = 90 b = 38.098 β = 101.72 c = 76.031 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 200 IMAGE PLATE RIGAKU RAXIS IV 2006-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 1.65 26.49 95.8 0.031 48.8 6.8 35314
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) 1.65 1.7 64.5 0.134 12.5 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2GSF 1.65 26.49 35314 1801 96.64 0.17 0.169 0.196 0.2113 RANDOM 16.354
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 30.383 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_3_deg 11.64 r_dihedral_angle_1_deg 5.144 r_scangle_it 2.38 r_scbond_it 1.641 r_angle_refined_deg 1.134 r_mcangle_it 1.01 r_mcbond_it 0.89 r_angle_other_deg 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.383 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_3_deg 11.64 r_dihedral_angle_1_deg 5.144 r_scangle_it 2.38 r_scbond_it 1.641 r_angle_refined_deg 1.134 r_mcangle_it 1.01 r_mcbond_it 0.89 r_angle_other_deg 0.838 r_symmetry_hbond_refined 0.294 r_symmetry_vdw_other 0.231 r_xyhbond_nbd_refined 0.229 r_nbd_refined 0.213 r_nbd_other 0.18 r_nbtor_refined 0.172 r_symmetry_vdw_refined 0.172 r_mcbond_other 0.148 r_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2387 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling