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The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Atomic resolution structure of Wild Type CcP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 30% 2-methyl-2,4-pentanediol (MPD), 50 mM Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.852 α = 90 b = 75.736 β = 90 c = 51.041 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 116 IMAGE PLATE MARRESEARCH mirrors 2003-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.78 SSRL BL9-1
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 1.13 100 98.5 0.061 27 8.625 189599 189599 2 2
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) 1.13 1.16 97.9 0.48 2.55
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 AB INITIO PHASING FREE R Atomic resolution structure of Wild Type CcP 1.13 10 153609 148486 5123 95.9 0.134 0.1471 0.1471 0.1773 0.1372 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 16 2223.1 2935.4
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.098 s_zero_chiral_vol 0.089 s_anti_bump_dis_restr 0.069 s_similar_adp_cmpnt 0.051 s_angle_d 0.03 s_from_restr_planes 0.0283 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2449 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 42
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling SHELX phasing