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Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 23)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 7 % PEG 8000, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane) pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.16 α = 90 b = 57.2 β = 109.8 c = 60.79 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 PIXEL DECTRIS PILATUS 6M-F 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 57.19 99.3 17.1 6.4 27358 37.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97 96.4 2.2 5
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 3WZD 2.09 57.19 19924 961 97.2 0.201 0.199 0.1992 0.234 0.2429 RANDOM 47.99
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] 1.0497 0.012 4.1851 -5.2347
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.67 t_omega_torsion 3.08 t_angle_deg 0.96 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 16.67 t_omega_torsion 3.08 t_angle_deg 0.96 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 2386 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction Aimless data scaling BUSTER refinement