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Crystal structure of Cytochrome C Peroxidase with a Proposed Electron Pathway Excised in a Complex with a Peptide Wire
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KXN PDB entry 1KXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 282 200 mM KPi, 25% MPD, pH 6.0, VAPOR DIFFUSION, temperature 282K
Crystal Properties Matthews coefficient Solvent content 3.05 59.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.029 α = 90 b = 75.07 β = 90 c = 50.79 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 IMAGE PLATE MARRESEARCH 2002-12-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.08 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 23.47 99.2 0.074 0.074 18.4 3.4 54795 54328 2 26.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 96.3 0.302 0.302 2.5 3.2 3857
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 (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 1KXN 1.6 10 54758 54073 2739 99.2 0.169 0.168 0.2126 0.19 0.2249 RANDOM 17.819
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] -0.26 0.29 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.26 r_dihedral_angle_4_deg 26.474 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 5.475 r_scangle_it 2.697 r_scbond_it 1.762 r_angle_refined_deg 1.344 r_mcangle_it 0.942 r_mcbond_it 0.581 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.26 r_dihedral_angle_4_deg 26.474 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 5.475 r_scangle_it 2.697 r_scbond_it 1.762 r_angle_refined_deg 1.344 r_mcangle_it 0.942 r_mcbond_it 0.581 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 43
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection AMoRE phasing