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Human Pantothenate kinase 3 in complex with a pantothenate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I7P pdb entry 2i7p
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Hepes, 0.005 M of each of ATP, magnesium chloride and N-heptylpantothenamide were also added, pH 7.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.63 α = 90 b = 99.63 β = 90 c = 69.62 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE RIGAKU RAXIS 2011-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.2 25 99.8 0.129 16.68 20590 -3 33.333
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 2.2 2.26 99.8 0.647 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2i7p 2.2 25 20508 1044 99.65 0.1926 0.19 0.2427 0.2098 RANDOM 25.5015
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] 0.75 0.38 0.75 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.969 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 5.945 r_scangle_it 2.772 r_scbond_it 1.765 r_angle_refined_deg 1.418 r_mcangle_it 1.129 r_angle_other_deg 0.904 r_mcbond_it 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.969 r_dihedral_angle_4_deg 16.146 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 5.945 r_scangle_it 2.772 r_scbond_it 1.765 r_angle_refined_deg 1.418 r_mcangle_it 1.129 r_angle_other_deg 0.904 r_mcbond_it 0.601 r_mcbond_other 0.135 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2692 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction