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Crystal structure of pantothenate synthetase in complex with 2-(5-methoxy-2-(naphthalen-2-ylsulfonylcarbamoyl)-1H-indol-1-yl)acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LE8 pdb entry 3LE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 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 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.72 α = 90 b = 70.86 β = 99.42 c = 81.83 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 325 mm CCD 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 1.75 21.429 99.9 0.062 13.1 3.7 204182 55392 23
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 1.75 1.84 99.9 0.586 2 3.6 8058
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 3LE8 1.75 21.429 52563 2810 99.82 0.17766 0.17506 0.1757 0.22664 0.227 RANDOM 28.626
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] 0.63 -0.36 1.29 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.147 r_dihedral_angle_4_deg 17.426 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 5.963 r_scangle_it 5.059 r_scbond_it 3.313 r_mcangle_it 2.161 r_angle_refined_deg 1.991 r_mcbond_it 1.325 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.147 r_dihedral_angle_4_deg 17.426 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 5.963 r_scangle_it 5.059 r_scbond_it 3.313 r_mcangle_it 2.161 r_angle_refined_deg 1.991 r_mcbond_it 1.325 r_chiral_restr 0.148 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4139 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 130
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling