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The structure of ascorbate peroxidase Compound III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAF PDB ENTRY 1OAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 LISO4 2.25M, HEPES 0.1M, PH8.3
Crystal Properties Matthews coefficient Solvent content 2.34 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.96 α = 90 b = 81.96 β = 90 c = 75.198 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.485 1.69 99.7 0.07 12.1 3.6 35606
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 1.485 1.524 99.2 0.42 2.11 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OAF 1.65 35.99 35606 1934 87.71 0.16352 0.16148 0.1489 0.20057 0.1912 RANDOM 23.785
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 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 26.575 r_dihedral_angle_3_deg 15.566 r_scangle_it 9.304 r_scbond_it 6.955 r_mcangle_it 5.485 r_dihedral_angle_1_deg 5.26 r_mcbond_it 3.971 r_angle_refined_deg 2.177 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.184 r_dihedral_angle_4_deg 26.575 r_dihedral_angle_3_deg 15.566 r_scangle_it 9.304 r_scbond_it 6.955 r_mcangle_it 5.485 r_dihedral_angle_1_deg 5.26 r_mcbond_it 3.971 r_angle_refined_deg 2.177 r_chiral_restr 0.064 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 1905 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling XDS phasing