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Expression, Purification, Characterization, and Solution NMR Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZBY PDB ENTRY 1ZBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.2M NH4Cl, 0.1 M CH3COONa pH5.0 and 20% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.052 α = 90 b = 87.92 β = 105.14 c = 87.526 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD RIGAKU SATURN 944+ 2011-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.39 50 99 0.158 91760 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.45 90.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1ZBY 2.39 43.57 2 24868 24481 1310 98.44 0.2156 0.21214 0.2129 0.27937 0.2796 RANDOM 30.992
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] 0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 21.677 r_dihedral_angle_3_deg 17.623 r_dihedral_angle_1_deg 6.389 r_scangle_it 3.692 r_scbond_it 2.396 r_angle_refined_deg 1.663 r_mcangle_it 1.463 r_mcbond_it 0.777 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 21.677 r_dihedral_angle_3_deg 17.623 r_dihedral_angle_1_deg 6.389 r_scangle_it 3.692 r_scbond_it 2.396 r_angle_refined_deg 1.663 r_mcangle_it 1.463 r_mcbond_it 0.777 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4704 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 88
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling