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Crystal structure of PPK2 (Class III) in complex with bisphosphonate inhibitor (2-((3,5-dichlorophenyl)amino)ethane-1,1-diyl)diphosphonic acid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1 M Phosphate Citrate pH 4.2
40% PEG 300
Crystal Properties Matthews coefficient Solvent content 3.78 67.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.355 α = 90 b = 109.355 β = 90 c = 179.737 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 2014-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 2.1 100 99.6 0.051 28.2 6.5 32073
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 2.1 2.141 100 0.59 1.91 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 93.42 30340 1622 99.25 0.18435 0.18247 0.22048 0.2283 RANDOM 55.396
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] 1.45 1.45 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.085 r_dihedral_angle_4_deg 23.382 r_dihedral_angle_3_deg 14.378 r_long_range_B_refined 7.345 r_long_range_B_other 7.345 r_dihedral_angle_1_deg 5.827 r_scangle_other 3.882 r_mcangle_it 2.49 r_mcangle_other 2.489 r_scbond_it 2.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.085 r_dihedral_angle_4_deg 23.382 r_dihedral_angle_3_deg 14.378 r_long_range_B_refined 7.345 r_long_range_B_other 7.345 r_dihedral_angle_1_deg 5.827 r_scangle_other 3.882 r_mcangle_it 2.49 r_mcangle_other 2.489 r_scbond_it 2.381 r_scbond_other 2.376 r_mcbond_it 1.563 r_mcbond_other 1.563 r_angle_refined_deg 1.491 r_angle_other_deg 0.931 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 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 2451 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing