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Crystal structure of the C-terminal domain from the catalase-peroxidase KatG of Escherichia coli (I41)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MWV pdb entry 1MWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 34% PEG 4000, 50 mM Sodium Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.235 α = 90 b = 59.235 β = 90 c = 160.382 γ = 90
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 4 Mirrors 2001-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.932 ESRF ID14-2
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 17.3 95.4 0.041 17719 17719
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) 1 2 2.1 93.5 0.15 2406
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1MWV 2 18 16817 16817 904 95.35 0.19206 0.19206 0.18912 0.24893 0.3036 RANDOM 23.001
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] -1.91 -1.91 3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.873 r_scangle_it 8.566 r_scbond_it 6.009 r_mcangle_it 4.453 r_mcbond_it 2.794 r_angle_refined_deg 1.751 r_symmetry_hbond_refined 0.309 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.873 r_scangle_it 8.566 r_scbond_it 6.009 r_mcangle_it 4.453 r_mcbond_it 2.794 r_angle_refined_deg 1.751 r_symmetry_hbond_refined 0.309 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2233 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing