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High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CYP PDB Entry 2CYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 30% 2-methyl-2,4-pentanediol (MPD), 50mM 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 = 106.673 α = 90 b = 75.513 β = 90 c = 50.994 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 110 IMAGE PLATE MARRESEARCH Mirrors 1999-07-04 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 1.2 100 96.8 0.071 12.2 10.05 1275193 126775 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) 1.2 1.22 74 0.437 1.99
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 2CYP 1.2 100 124130 120831 3116 96.2 0.1162 0.1132 0.1132 0.1087 0.1495 0.11 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 18 2222 3123
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.118 s_non_zero_chiral_vol 0.093 s_zero_chiral_vol 0.082 s_anti_bump_dis_restr 0.063 s_similar_adp_cmpnt 0.048 s_angle_d 0.029 s_from_restr_planes 0.0279 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2409 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 43
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction DPS data reduction MOSFLM data reduction SHELX phasing