☰ Navigation Tabs
cytochrome c peroxidase: 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 3.02 59.24
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 1.86 39.13 90.4 0.06 18 3.8 31259 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 1.86 1.96 92.3 0.27 3.4 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V23 1.86 36.84 29663 1553 89.66 0.21357 0.21179 0.24693 0.2333 RANDOM 17.878
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_4_deg 26.11 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 6.375 r_scangle_it 3.767 r_scbond_it 2.775 r_angle_refined_deg 1.865 r_mcangle_it 1.69 r_mcbond_it 1.13 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.138 r_dihedral_angle_4_deg 26.11 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 6.375 r_scangle_it 3.767 r_scbond_it 2.775 r_angle_refined_deg 1.865 r_mcangle_it 1.69 r_mcbond_it 1.13 r_chiral_restr 0.143 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 126 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing