☰ Navigation Tabs
Pantothenate synthetase in complex with racemate (2S)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID and (2R)-2,3-DIHYDRO-1,4-BENZODIOXINE-2-CARBOXYLIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 11-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.41 α = 90 b = 70.99 β = 99.58 c = 81.68 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.97 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 2.33 47.73 98.6 0.113 7.5 3.6 83193 23179 31.7
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 2.33 2.46 90.7 0.477 2.6 3.3 10122
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 3COV 2.33 47.73 21974 1191 98.61 0.17382 0.17012 0.1683 0.2399 0.2351 RANDOM 31.857
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] 0.94 1.32 1.72 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_4_deg 16.881 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 6.255 r_scangle_it 4.216 r_scbond_it 2.633 r_mcangle_it 1.701 r_angle_refined_deg 1.661 r_mcbond_it 0.935 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_4_deg 16.881 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 6.255 r_scangle_it 4.216 r_scbond_it 2.633 r_mcangle_it 1.701 r_angle_refined_deg 1.661 r_mcbond_it 0.935 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4076 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement