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Room temperature structure of Ascorbate Peroxidase at 1.54A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298.7 0.1M Tris HCl, 2.7M Magnesium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.831 α = 90 b = 82.831 β = 90 c = 76.017 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 298.7 PIXEL RIGAKU HyPix-6000HE 2025-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.54 29.29 99.9 0.997 8.8 11.3 42926
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.54 0.999
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.54 28.019 42877 2119 99.9 0.168 0.1667 0.1732 0.2013 0.2051 RANDOM 16.646
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] -0.63 -0.63 1.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.901 r_dihedral_angle_2_deg 12.706 r_dihedral_angle_3_deg 12.176 r_lrange_other 9.933 r_lrange_it 9.911 r_scangle_it 9.106 r_scangle_other 9.103 r_rigid_bond_restr 6.613 r_scbond_other 6.4 r_scbond_it 6.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.901 r_dihedral_angle_2_deg 12.706 r_dihedral_angle_3_deg 12.176 r_lrange_other 9.933 r_lrange_it 9.911 r_scangle_it 9.106 r_scangle_other 9.103 r_rigid_bond_restr 6.613 r_scbond_other 6.4 r_scbond_it 6.384 r_dihedral_angle_1_deg 6.004 r_mcangle_it 5.274 r_mcangle_other 5.272 r_mcbond_other 3.554 r_mcbond_it 3.553 r_angle_refined_deg 1.939 r_dihedral_angle_other_2_deg 1.055 r_angle_other_deg 0.678 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.217 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.179 r_nbd_other 0.16 r_chiral_restr 0.106 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1904 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction CrysalisPro data scaling PHASER phasing