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Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU385595
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 0.2 M Sodium fluoride, 18% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.86 33.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.2 α = 71.73 b = 52.46 β = 85.98 c = 69.36 γ = 64.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 65.7 96.5 0.081 0.054 0.99 7.9 3 37626
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 2.05 0.296 0.2 0.929
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 6UJ5 2 65.68 37626 1882 96.5 0.18 0.1772 0.1772 0.237 0.2337 RANDOM 27.622
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] 0.44 1.13 -0.32 -2.44 0.42 3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.986 r_dihedral_angle_4_deg 19.227 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_1_deg 6.696 r_angle_refined_deg 1.533 r_chiral_restr 0.105 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5095 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing