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Kinase domain of human EphB1, G703C mutant, covalently bound to a quinazoline-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18 % PEG3350, 0.1-0.2 M ammonium sulfate and 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) buffer pH 6-9
Crystal Properties Matthews coefficient Solvent content 3.42 64.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.2 α = 90 b = 102.2 β = 90 c = 157.55 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M-F 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.23 58.84 100 0.106 0.997 10.2 9.7 47109 51.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.29 100 1.707 0.622 1.6 10.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZFX 2.23 58.84 46452 2232 98.7 0.199 0.198 0.1965 0.214 0.2099 RANDOM 59.29
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] 0.8447 0.8447 -1.6895
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.08 t_omega_torsion 3.23 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.08 t_omega_torsion 3.23 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4354 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 135
Software Software Software Name Purpose BUSTER refinement DIALS data reduction Aimless data scaling PHASER phasing