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Crystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 297 0.6 M sodium chloride, 9% PEG 6000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.633 α = 90 b = 84.079 β = 90 c = 143.539 γ = 90
Symmetry Space Group P 21 21 21
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 2M-F 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.17 50 99.9 20.9 6.2 47245
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 THROUGHOUT 5CSR 2.17 50 44788 2391 99.66 0.18516 0.18308 0.1922 0.2245 0.2333 RANDOM 34.162
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] -1.27 0.78 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 17.541 r_dihedral_angle_3_deg 13.843 r_long_range_B_refined 8.564 r_long_range_B_other 8.564 r_scangle_other 6.548 r_dihedral_angle_1_deg 5.638 r_mcangle_it 4.24 r_mcangle_other 4.24 r_scbond_it 4.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 17.541 r_dihedral_angle_3_deg 13.843 r_long_range_B_refined 8.564 r_long_range_B_other 8.564 r_scangle_other 6.548 r_dihedral_angle_1_deg 5.638 r_mcangle_it 4.24 r_mcangle_other 4.24 r_scbond_it 4.152 r_scbond_other 4.152 r_mcbond_it 2.849 r_mcbond_other 2.848 r_angle_refined_deg 1.55 r_angle_other_deg 1.425 r_chiral_restr 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6640 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing