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Type III pantothenate kinase from Thermotoga maritima complexed with pantothenate and ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.962 α = 90 b = 136.685 β = 109.71 c = 75.01 γ = 90
Symmetry Space Group P 1 21 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 IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 50 98.9 0.066 58933
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 50 58933 3156 98.63 0.19363 0.19027 0.1871 0.25696 0.2537 RANDOM 21.275
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] 0.2 0.19 -0.2 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 15.339 r_dihedral_angle_1_deg 5.398 r_scangle_it 1.973 r_angle_refined_deg 1.409 r_scbond_it 1.141 r_mcangle_it 0.853 r_mcbond_it 0.497 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 20.046 r_dihedral_angle_3_deg 15.339 r_dihedral_angle_1_deg 5.398 r_scangle_it 1.973 r_angle_refined_deg 1.409 r_scbond_it 1.141 r_mcangle_it 0.853 r_mcbond_it 0.497 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.233 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.189 r_chiral_restr 0.159 r_xyhbond_nbd_refined 0.146 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11574 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling