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cytochrome c peroxidase: ascorbate bound to the engineered ascorbate binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V23 PDB ENTRY 2V23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 DIALYSIS AGAINST PHOSPHATE BUFFER 50 MM PH 6, MPD 30%
Crystal Properties Matthews coefficient Solvent content 2.78 55.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 74.49 β = 90 c = 106.47 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 RIGAKU-MSC XENOCS 2008-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 29.48 97.3 0.09 14.1 2.9 25406 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 2.11 98.5 0.35 1.7 2.7
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2V23 2.01 41.92 25808 100 0.20148 0.20148 0.3478 27.38
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] -0.33 0.5 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 22.113 r_dihedral_angle_3_deg 13.892 r_dihedral_angle_1_deg 6.413 r_scangle_it 3.269 r_scbond_it 2.467 r_angle_refined_deg 1.637 r_mcangle_it 1.46 r_mcbond_it 0.993 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.189 r_dihedral_angle_4_deg 22.113 r_dihedral_angle_3_deg 13.892 r_dihedral_angle_1_deg 6.413 r_scangle_it 3.269 r_scbond_it 2.467 r_angle_refined_deg 1.637 r_mcangle_it 1.46 r_mcbond_it 0.993 r_nbtor_refined 0.306 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing