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Monoclinic triose phosphate isomerase from Fasciola hepatica.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 0.2 M Li2SO4, 0.1 M ADA pH 6.5, 30 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.393 α = 90 b = 110.464 β = 97.367 c = 118.143 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 PIXEL DECTRIS PILATUS 6M-F 2015-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.51 51.809 99.1 0.059 0.999 10.9 3.2 167030
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 1.457 0.321
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2JK2 1.51 51.809 166994 8336 99.073 0.167 0.1651 0.1652 0.1932 0.1933 27.833
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] -0.797 0.712 0.347 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.041 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 13.901 r_lrange_it 10.192 r_lrange_other 10.133 r_scangle_it 8.68 r_scangle_other 8.68 r_scbond_it 6.29 r_scbond_other 6.272 r_dihedral_angle_1_deg 6.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.041 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 13.901 r_lrange_it 10.192 r_lrange_other 10.133 r_scangle_it 8.68 r_scangle_other 8.68 r_scbond_it 6.29 r_scbond_other 6.272 r_dihedral_angle_1_deg 6.269 r_mcangle_it 6.02 r_mcangle_other 6.014 r_mcbond_it 4.499 r_mcbond_other 4.491 r_angle_refined_deg 1.41 r_angle_other_deg 1.351 r_metal_ion_refined 0.272 r_nbd_other 0.271 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.214 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_other 0.149 r_symmetry_xyhbond_nbd_refined 0.137 r_ncsr_local_group_2 0.095 r_ncsr_local_group_6 0.091 r_ncsr_local_group_4 0.085 r_ncsr_local_group_5 0.084 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.079 r_chiral_restr 0.07 r_ncsr_local_group_3 0.069 r_bond_refined_d 0.008 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 7766 Nucleic Acid Atoms Solvent Atoms 1090 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PARROT phasing MoRDa phasing