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Crystal structure of PAK2 kinase domain containing D368N mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Na citrate, pH 6.5, 0.65 M Li2SO4, 0.3 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.529 α = 90 b = 97.529 β = 90 c = 144.962 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS3 6M 2012-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50 99.9 0.117 0.124 0.039 0.988 22.4 9.9 16624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.678 0.744 1.6 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 46.219 16599 803 99.772 0.243 0.2425 0.2449 0.2628 0.2646 82.772
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] -3.698 -1.849 -3.698 11.997
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.072 r_lrange_other 21.072 r_scangle_other 14.269 r_scangle_it 14.248 r_dihedral_angle_6_deg 14.032 r_dihedral_angle_3_deg 13.475 r_mcangle_it 13.11 r_mcangle_other 13.105 r_scbond_it 9.165 r_scbond_other 9.008
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.072 r_lrange_other 21.072 r_scangle_other 14.269 r_scangle_it 14.248 r_dihedral_angle_6_deg 14.032 r_dihedral_angle_3_deg 13.475 r_mcangle_it 13.11 r_mcangle_other 13.105 r_scbond_it 9.165 r_scbond_other 9.008 r_mcbond_it 8.753 r_mcbond_other 8.725 r_dihedral_angle_1_deg 6.694 r_dihedral_angle_2_deg 5.135 r_angle_refined_deg 1.635 r_angle_other_deg 0.52 r_symmetry_nbd_refined 0.327 r_nbd_refined 0.24 r_nbd_other 0.238 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing