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Crystal structure of PPK3 Class III in complex with inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 292 0.1 M phosphate citrate pH 4.2
40% PEG 300
Crystal Properties Matthews coefficient Solvent content 3.84 67.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.475 α = 90 b = 111.475 β = 90 c = 175.733 γ = 90
Symmetry Space Group I 41 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 CCD ADSC QUANTUM 315r 2013-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 100 99.6 0.08 0.023 32.8 14.3 24690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 1.54 0.43 2.3 13.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FREE R-VALUE 2.3 94.13 21885 1169 92.74 0.1933 0.19073 0.1988 0.24101 0.2398 RANDOM 40.28
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.251 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 16.91 r_dihedral_angle_1_deg 6.657 r_long_range_B_refined 6.073 r_long_range_B_other 6.073 r_scangle_other 2.7 r_mcangle_it 2.227 r_mcangle_other 2.226 r_scbond_it 1.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.251 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 16.91 r_dihedral_angle_1_deg 6.657 r_long_range_B_refined 6.073 r_long_range_B_other 6.073 r_scangle_other 2.7 r_mcangle_it 2.227 r_mcangle_other 2.226 r_scbond_it 1.571 r_scbond_other 1.569 r_angle_refined_deg 1.544 r_mcbond_it 1.29 r_mcbond_other 1.29 r_angle_other_deg 0.938 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2446 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing