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Crystal structure of the C-terminal domain from the catalase-peroxidase KatG of Escherichia coli (P21 21 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U2K pdb entry 1u2k
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.6 M Sodium Citrate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.208 α = 90 b = 98.699 β = 90 c = 302.821 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 4 Mirrors 2001-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97395 ESRF ID14-4
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 20 91.4 0.087 135504 135504
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 2.2 92.8 0.18 17775
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1u2k 2.3 19.96 92771 92771 10340 100 0.24264 0.24264 0.2332 0.2511 0.32668 0.3162 RANDOM 26.123
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] -0.85 -1.03 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.75 r_scangle_it 6.601 r_scbond_it 4.808 r_mcangle_it 3.517 r_mcbond_it 2.044 r_angle_refined_deg 1.359 r_symmetry_hbond_refined 0.525 r_symmetry_vdw_refined 0.442 r_nbd_refined 0.303 r_xyhbond_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.75 r_scangle_it 6.601 r_scbond_it 4.808 r_mcangle_it 3.517 r_mcbond_it 2.044 r_angle_refined_deg 1.359 r_symmetry_hbond_refined 0.525 r_symmetry_vdw_refined 0.442 r_nbd_refined 0.303 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 18136 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing