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Crystal structure of the catalase-peroxidase from Neurospora crassa at 2.6 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I05 PDB entry 5I05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 9% PEG 8,000, 225 mM magnesium chloride and 100 mM Tris-HCl, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.87 57.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.81 α = 90 b = 142.35 β = 90 c = 183.11 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 210r 2017-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9 APS 19-BM
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 2.6 112.38 99.5 0.069 8.6 6.5 58654 28.4
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 2.6 2.74 99.3 0.59 2.8 5.5
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 FREE R-VALUE PDB entry 5I05 2.6 112.38 56550 2000 99.9 0.21 0.209 0.2122 0.254 0.2557 RANDOM 28.66
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] -0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 20.673 r_dihedral_angle_3_deg 20.105 r_dihedral_angle_1_deg 3.311 r_angle_refined_deg 1.959 r_angle_other_deg 1.357 r_chiral_restr 0.149 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 20.673 r_dihedral_angle_3_deg 20.105 r_dihedral_angle_1_deg 3.311 r_angle_refined_deg 1.959 r_angle_other_deg 1.357 r_chiral_restr 0.149 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 11196 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing