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Crystal Structure of A Pantothenate synthetase complexed with AMP
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 = 120.262 α = 90 b = 44.944 β = 125.56 c = 82.236 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 mirrors 2004-01-01 M 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) 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 1.7 50 88 0.039 0.039 33.8 4.2 34940 34940 -3 -3 23.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 47 0.22 0.22 5.2 3.1 1835
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 1.7 20 32094 32094 2802 88.13 0.15043 0.15043 0.14831 0.1543 0.17456 0.1827 RANDOM 31.613
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] -0.2 0.07 0.37 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 12.827 r_scangle_it 7.143 r_dihedral_angle_1_deg 5.259 r_scbond_it 4.957 r_mcangle_it 3.372 r_mcbond_it 2.52 r_angle_refined_deg 1.673 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 12.827 r_scangle_it 7.143 r_dihedral_angle_1_deg 5.259 r_scbond_it 4.957 r_mcangle_it 3.372 r_mcbond_it 2.52 r_angle_refined_deg 1.673 r_nbtor_refined 0.311 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.138 r_xyhbond_nbd_refined 0.135 r_bond_refined_d 0.018 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 2034 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing