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Oxidised Thiol peroxidase (Tpx) from Yersinia pseudotuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXH PDB ENTRY 1QXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M TRI-POTASSIUM CITRATE, 20% PEG 3350, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.371 α = 90 b = 63.444 β = 90 c = 91.394 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 CCD MIRRORS 2010-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 38.27 99.9 0.14 8.6 13.54 11830 2 45.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.47 4 14.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1QXH 2.5 52.118 2.5 11814 558 99.738 0.301 0.2989 0.2944 0.3358 0.3233 RANDOM 51.88
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] -7.948 4.954 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.07 r_dihedral_angle_3_deg 16.981 r_dihedral_angle_4_deg 13.647 r_dihedral_angle_1_deg 4.42 r_angle_refined_deg 0.92 r_scangle_it 0.544 r_mcangle_it 0.42 r_scbond_it 0.309 r_nbtor_refined 0.294 r_mcbond_it 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.07 r_dihedral_angle_3_deg 16.981 r_dihedral_angle_4_deg 13.647 r_dihedral_angle_1_deg 4.42 r_angle_refined_deg 0.92 r_scangle_it 0.544 r_mcangle_it 0.42 r_scbond_it 0.309 r_nbtor_refined 0.294 r_mcbond_it 0.229 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.092 r_symmetry_hbond_refined 0.055 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling PHASER phasing