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Crystal structure of the kinase domain of human PAK1 in complex with compound 15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.4 α = 90 b = 83.36 β = 105.04 c = 66.02 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 2M 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 Diamond I04
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 2.49 83.36 97.6 0.041 14.4 2.9 64319 22335 71.55
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 2.49 2.63 96.7 0.569 1.4 2.7
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 1YHV 2.49 50.64 22308 1147 96.99 0.2094 0.2085 0.2231 0.2253 0.2416 RANDOM 87.18
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] -7.7659 -13.929 2.1586 5.6073
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.66 t_omega_torsion 2.93 t_angle_deg 1.15 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 19.66 t_omega_torsion 2.93 t_angle_deg 1.15 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 4187 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 62
Software Software Software Name Purpose BUSTER refinement