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Structure of Sorghum peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BGP PDB ENTRY 1BGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 100 MM SODIUM PHOSPHATE 4 M SODIUM FORMATE PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.95 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.62 α = 90 b = 58.62 β = 90 c = 208.41 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PIXEL 2012-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.27 36.36 98.4 0.03 19.4 5.4 103499
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 1.27 5.7 93.9 0.7 2.1 4.9
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 1BGP 1.27 36.36 103499 5440 98.33 0.13728 0.13612 0.1481 0.15931 0.1712 RANDOM 27.047
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] 0.51 0.25 0.51 -1.64
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.902 r_dihedral_angle_2_deg 32.531 r_dihedral_angle_4_deg 19.564 r_sphericity_bonded 17.923 r_dihedral_angle_3_deg 11.854 r_rigid_bond_restr 7.266 r_dihedral_angle_1_deg 6.387 r_scbond_it 5.434 r_mcangle_it 3.984 r_mcbond_it 3.64
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.902 r_dihedral_angle_2_deg 32.531 r_dihedral_angle_4_deg 19.564 r_sphericity_bonded 17.923 r_dihedral_angle_3_deg 11.854 r_rigid_bond_restr 7.266 r_dihedral_angle_1_deg 6.387 r_scbond_it 5.434 r_mcangle_it 3.984 r_mcbond_it 3.64 r_mcbond_other 3.632 r_angle_refined_deg 1.478 r_angle_other_deg 1.219 r_chiral_restr 0.135 r_gen_planes_refined 0.017 r_gen_planes_other 0.015 r_bond_refined_d 0.01 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing