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Crystal structure of PPK2 Class III in the complex with AMP from Cytophaga hutchinsonii ATCC 33406
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 0.8 Ammonium Sulfate
0.1M NaCL
0.1 M Sodium Citrate:HCl pH 4
Crystal Properties Matthews coefficient Solvent content 3.89 68.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.224 α = 90 b = 111.224 β = 90 c = 177.694 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 2016-01-01 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) 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 2.45 40 98.5 0.12 12 5.6 20573
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49
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 3RHF 2.45 39.32 17937 966 90.57 0.19115 0.18955 0.1951 0.22018 0.2221 RANDOM 38.458
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.815 r_dihedral_angle_4_deg 28.13 r_dihedral_angle_3_deg 19.261 r_long_range_B_refined 10.66 r_long_range_B_other 10.656 r_scangle_other 8.145 r_mcangle_other 5.185 r_mcangle_it 5.181 r_scbond_it 5.123 r_scbond_other 5.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.815 r_dihedral_angle_4_deg 28.13 r_dihedral_angle_3_deg 19.261 r_long_range_B_refined 10.66 r_long_range_B_other 10.656 r_scangle_other 8.145 r_mcangle_other 5.185 r_mcangle_it 5.181 r_scbond_it 5.123 r_scbond_other 5.121 r_dihedral_angle_1_deg 4.298 r_mcbond_it 3.457 r_mcbond_other 3.437 r_angle_refined_deg 1.707 r_angle_other_deg 1.076 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 2410 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing