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Crystal structure of triosephosphate isomerase from Thermoplasma acidophilium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 297 0.5 M sodium chloride, 10% PEG 6000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.486 α = 90 b = 113.963 β = 90 c = 114.796 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 CCD ADSC QUANTUM 270 2013-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.0 PAL/PLS 7A (6B, 6C1)
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 1.94 50 99 32.4 7.1 73921
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 1HG3 1.94 50 70068 3707 99.64 0.18191 0.18014 0.1937 0.21541 0.2234 RANDOM 33.2
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] 1.68 -0.31 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.875 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 11.966 r_long_range_B_refined 7.954 r_long_range_B_other 7.785 r_scangle_other 6.142 r_dihedral_angle_1_deg 5.824 r_scbond_it 3.994 r_scbond_other 3.994 r_mcangle_it 3.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.875 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 11.966 r_long_range_B_refined 7.954 r_long_range_B_other 7.785 r_scangle_other 6.142 r_dihedral_angle_1_deg 5.824 r_scbond_it 3.994 r_scbond_other 3.994 r_mcangle_it 3.754 r_mcangle_other 3.754 r_mcbond_other 2.719 r_mcbond_it 2.718 r_angle_refined_deg 1.648 r_angle_other_deg 1.389 r_chiral_restr 0.103 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.008 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 6764 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing