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Pantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-yl acetic 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 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.58 α = 90 b = 70.93 β = 99.4 c = 82.01 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 CCD MARMOSAIC 225 mm CCD 2008-06-17 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) 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 2.07 53.38 99.8 0.123 0.122 13.8 4.4 148474 33607 4
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 2.07 2.18 100 0.499 4
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 3COV 2.07 53.38 33657 31727 1693 99.34 0.19022 0.18705 0.1865 0.24987 0.2481 RANDOM 26.386
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] 0.82 -0.26 1.26 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.74 r_dihedral_angle_4_deg 18.096 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_1_deg 6.787 r_scangle_it 4.663 r_scbond_it 3.087 r_angle_refined_deg 1.996 r_mcangle_it 1.861 r_mcbond_it 1.113 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.74 r_dihedral_angle_4_deg 18.096 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_1_deg 6.787 r_scangle_it 4.663 r_scbond_it 3.087 r_angle_refined_deg 1.996 r_mcangle_it 1.861 r_mcbond_it 1.113 r_chiral_restr 0.127 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4174 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 75
Software Software Software Name Purpose DNA data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling