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Structure of PAK2 in complex with compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 3350, 200 mM Ammonium tartrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.629 α = 90 b = 80.755 β = 106.186 c = 66.742 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 EIGER X 9M 2021-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 2.1 47.783 98.6 0.091 0.996 7.4 7.5 36183
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 2.1 2.16 98.4 1.405 0.657 0.8 7.7
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 2.1 47.783 36165 1790 98.349 0.215 0.2117 0.215 0.2855 0.2843 72.645
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] -0.441 -0.511 -0.567 1.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.429 r_dihedral_angle_2_deg 16.352 r_dihedral_angle_6_deg 15.78 r_lrange_other 12.19 r_lrange_it 12.168 r_scangle_other 10.39 r_scangle_it 10.377 r_mcangle_it 9.282 r_mcangle_other 9.281 r_dihedral_angle_1_deg 8.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.429 r_dihedral_angle_2_deg 16.352 r_dihedral_angle_6_deg 15.78 r_lrange_other 12.19 r_lrange_it 12.168 r_scangle_other 10.39 r_scangle_it 10.377 r_mcangle_it 9.282 r_mcangle_other 9.281 r_dihedral_angle_1_deg 8.387 r_scbond_it 8.008 r_scbond_other 7.983 r_mcbond_it 7.467 r_mcbond_other 7.464 r_angle_refined_deg 2.592 r_angle_other_deg 0.817 r_symmetry_xyhbond_nbd_refined 0.338 r_nbd_refined 0.225 r_ncsr_local_group_1 0.224 r_symmetry_nbd_other 0.217 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.209 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.129 r_chiral_restr 0.123 r_symmetry_nbtor_other 0.094 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.014 r_chiral_restr_other 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4510 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing