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Crystal structure of E. coli HPII catalase variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BFL PDB entry 4BFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2% PEG20000, 15% PEG5000 MME, 0.1 M potassium chloride, 0.1 M manganese acetate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.789 α = 90 b = 171.331 β = 121.55 c = 122.484 γ = 90
Symmetry Space Group C 1 2 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 315r 2014-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A
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 1.5 50 67.7 0.07 14.63 4.2 451438 305824
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 0.46
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 4BFL 1.53 50 290638 15186 71.79 0.08475 0.08228 0.0823 0.13211 0.1322 RANDOM 18.036
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] 0.66 0.21 -0.59 -0.19
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.426 r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 14.576 r_dihedral_angle_3_deg 12.809 r_sphericity_bonded 12.211 r_long_range_B_refined 6.079 r_long_range_B_other 6.079 r_dihedral_angle_1_deg 5.935 r_scangle_other 2.971 r_scbond_it 2.548
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.426 r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 14.576 r_dihedral_angle_3_deg 12.809 r_sphericity_bonded 12.211 r_long_range_B_refined 6.079 r_long_range_B_other 6.079 r_dihedral_angle_1_deg 5.935 r_scangle_other 2.971 r_scbond_it 2.548 r_scbond_other 2.545 r_mcangle_it 1.904 r_mcangle_other 1.904 r_rigid_bond_restr 1.691 r_mcbond_it 1.527 r_mcbond_other 1.527 r_angle_refined_deg 1.502 r_angle_other_deg 1.107 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23559 Nucleic Acid Atoms Solvent Atoms 4669 Heterogen Atoms 535
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing