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Structure of the pantothenate kinase (coaA) from Coxiella burnetii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ESM PDB CODE 1ESM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 298 0.2 M sodium chloride, 10% PEG8000, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.214 α = 90 b = 94.698 β = 106.4 c = 75.398 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 CCD MAR CCD 165 mm 2011-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.3 100 93.9 0.062 22.2 4 51888 46728 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 91 0.306 4.5 3.8 2552
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB CODE 1ESM 2.3 72.33 37970 35570 1802 93.68 0.21381 0.2109 0.2156 0.26861 0.271 RANDOM 30.956
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] 0.15 -0.34 -1.9 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.683 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 14.877 r_dihedral_angle_1_deg 5.591 r_scangle_it 2.51 r_scbond_it 1.541 r_angle_refined_deg 1.247 r_mcangle_it 0.882 r_angle_other_deg 0.831 r_mcbond_it 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.683 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 14.877 r_dihedral_angle_1_deg 5.591 r_scangle_it 2.51 r_scbond_it 1.541 r_angle_refined_deg 1.247 r_mcangle_it 0.882 r_angle_other_deg 0.831 r_mcbond_it 0.453 r_mcbond_other 0.103 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4994 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling