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Crystal structure of the catalase-peroxidase from Neurospora crassa at 2.9 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 BATCH MODE 7 291 0.2 M calcium acetate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.306 α = 90 b = 115.648 β = 90 c = 123.035 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 PIXEL DECTRIS PILATUS 6M 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.85 APS 19-ID
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 2.9 84.27 97.3 0.075 5.2 4 30732 50.3
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 2.9 3.06 94.2 0.59 2.4 3.7
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 2.9 84.27 30732 1652 96.21 0.2277 0.2239 0.226 0.2966 0.297 RANDOM 45.318
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] -0.05 0.31 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 22.099 r_dihedral_angle_3_deg 20.858 r_dihedral_angle_1_deg 4.509 r_angle_refined_deg 1.653 r_angle_other_deg 1.208 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 22.099 r_dihedral_angle_3_deg 20.858 r_dihedral_angle_1_deg 4.509 r_angle_refined_deg 1.653 r_angle_other_deg 1.208 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11160 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing