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Crystal structure of recombinant class II fumarase from Schistosoma mansoni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 294 Sodium acetate pH 4, sodium L-malate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.65 α = 90 b = 67.86 β = 118.61 c = 187.27 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 PIXEL DECTRIS EIGER X 9M 2019-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 46.93 98.6 0.997 11.2 6.8 167349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 0.552
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 FREE R-VALUE 5d6b 1.85 46.93 158981 8368 98.54 0.1936 0.1918 0.1936 0.2271 0.2291 RANDOM 29.562
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] 2.19 0.58 -1.51 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 14.471 r_dihedral_angle_3_deg 13.299 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 1.349 r_angle_other_deg 1.298 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 14.471 r_dihedral_angle_3_deg 13.299 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 1.349 r_angle_other_deg 1.298 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14331 Nucleic Acid Atoms Solvent Atoms 900 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing