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Crystal structure of A Pantothenate synthetase complexed with AMP and beta-alanine
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, ethanol, magnesium chloride, lithium sulfate, imidazole, pH 8.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.991 α = 90 b = 70.64 β = 99.21 c = 81.683 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 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 1.85 50 0.083 23.6 2.7 45909 45909 -3 -3
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 1.85 1.9 98.1 0.547 2.5 2.2
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 pdb entry 1MOP 1.85 20 45884 42160 3724 99.8 0.16074 0.15769 0.1601 0.19529 0.198 RANDOM 33.451
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] 1.35 -0.55 0.61 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.974 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_1_deg 5.867 r_scangle_it 4.392 r_scbond_it 2.825 r_mcangle_it 1.699 r_angle_refined_deg 1.67 r_mcbond_it 1.143 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.974 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 14.561 r_dihedral_angle_1_deg 5.867 r_scangle_it 4.392 r_scbond_it 2.825 r_mcangle_it 1.699 r_angle_refined_deg 1.67 r_mcbond_it 1.143 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 4172 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing