☰ Navigation Tabs
Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 2.4M Na Malonate pH 6.5, 0.1M TCEP HCl
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.874 α = 90 b = 109.717 β = 90 c = 142.571 γ = 90
Symmetry Space Group P 21 21 21
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 2015-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.14 50 100 0.15 0.157 0.057 5.1 8.1 96028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 100 0.94 0.351 0.791 8.1 4721
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 3SMS 2.14 50.01 93190 1462 99.98 0.2146 0.214 0.2179 0.2505 0.249 RANDOM 34.084
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] 0.66 0.75 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.273 r_dihedral_angle_4_deg 16.993 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 5.825 r_mcangle_it 2.122 r_mcbond_it 1.34 r_mcbond_other 1.34 r_angle_refined_deg 1.282 r_angle_other_deg 0.897 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.273 r_dihedral_angle_4_deg 16.993 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 5.825 r_mcangle_it 2.122 r_mcbond_it 1.34 r_mcbond_other 1.34 r_angle_refined_deg 1.282 r_angle_other_deg 0.897 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11071 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 191
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-3000 data reduction