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Escherichia coli Thiol peroxidase (Tpx) resolving cysteine to serine mutant (C95S) with an intermolecular disulfide bond
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HVV pdb entry 3HVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 15% (w/v) PEG 8000, 0.1 M Tris, 0.2 M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.719 α = 90 b = 123.362 β = 103.01 c = 61.932 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 CCD ADSC QUANTUM 210 2008-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.978 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 62 96.6 0.062 10.7 2.7 32466
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 90.7 0.22 3.3 2.1 2229
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 pdb entry 3HVV 2.12 61.66 32466 3598 96.63 0.1707 0.16226 0.1812 0.24784 0.2584 RANDOM 12.428
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] 0.03 0.4 0.08 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.665 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 16.202 r_dihedral_angle_1_deg 6.985 r_scangle_it 5.538 r_mcangle_it 4.505 r_scbond_it 4.176 r_mcbond_it 3.463 r_angle_refined_deg 1.588 r_mcbond_other 1.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.665 r_dihedral_angle_4_deg 20.557 r_dihedral_angle_3_deg 16.202 r_dihedral_angle_1_deg 6.985 r_scangle_it 5.538 r_mcangle_it 4.505 r_scbond_it 4.176 r_mcbond_it 3.463 r_angle_refined_deg 1.588 r_mcbond_other 1.268 r_angle_other_deg 0.899 r_chiral_restr 0.1 r_bond_refined_d 0.019 r_gen_planes_refined 0.018 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 11
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling