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Crystal structure of A Pantothenate synthetase complexed with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MOP PDB entry 1MOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 3000, glycerol, isopropanol, magnesium chloride, lithium sulfate, imidazole, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.953 α = 90 b = 44.877 β = 125.26 c = 82.125 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
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 1.55 50 87.6 0.06 30.7 6.6 45287 45287 -3 -3 24.5
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 1.55 1.61 30.8 30.8 0.343 3.9 3.5 1580
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 (All) 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 1MOP 1.55 20 45261 45261 3683 87.77 0.152 0.152 0.15 0.1515 0.169 0.1686 RANDOM 26.429
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] 0.36 0.25 -0.1 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.284 r_dihedral_angle_4_deg 13.897 r_dihedral_angle_3_deg 11.968 r_scangle_it 6.314 r_dihedral_angle_1_deg 5.197 r_scbond_it 4.491 r_mcangle_it 2.988 r_mcbond_it 2.653 r_angle_refined_deg 1.599 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.284 r_dihedral_angle_4_deg 13.897 r_dihedral_angle_3_deg 11.968 r_scangle_it 6.314 r_dihedral_angle_1_deg 5.197 r_scbond_it 4.491 r_mcangle_it 2.988 r_mcbond_it 2.653 r_angle_refined_deg 1.599 r_angle_other_deg 0.827 r_mcbond_other 0.618 r_symmetry_vdw_other 0.246 r_nbd_refined 0.216 r_nbd_other 0.189 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.098 r_nbtor_other 0.083 r_metal_ion_refined 0.026 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2040 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing