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Crystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(5-Methylpyridin-2-ylsulfonylcarbamoyl)-1H-indol-1-yl) acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COW PDB ENTRY 3COW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 12-14% PEG 3000, 100-150 mM Li2SO4, 100-150 mM imidazole, 2-4% Ethanol, 5-10% Glycerol,20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.55 α = 90 b = 70.71 β = 99.37 c = 81.84 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 MARMOSAIC 225 mm CCD 2009-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99 SLS X06DA
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 1.73 27.68 99.9 0.079 11.9 3.7 57085 19.5
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 1.73 1.82 100 0.539 2.1 3.6 8321
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 PDB ENTRY 3COW 1.73 27.68 54175 2891 99.93 0.1743 0.17247 0.1719 0.20755 0.2088 RANDOM 22.212
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] 0.42 -0.58 0.74 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.264 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_1_deg 5.771 r_scangle_it 3.476 r_scbond_it 2.162 r_angle_refined_deg 1.49 r_mcangle_it 1.455 r_mcbond_it 0.91 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.264 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_1_deg 5.771 r_scangle_it 3.476 r_scbond_it 2.162 r_angle_refined_deg 1.49 r_mcangle_it 1.455 r_mcbond_it 0.91 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 4159 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 172
Software Software Software Name Purpose PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling