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Crystal Structure of a Fungal DyP-Type Peroxidase from Auricularia auricula-judae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D3Q PDB ENTRY 2D3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.17 M SODIUM ACETATE TRIHYDRATE 0.085 M TRIS HYDROCHLORIDE PH 8.5 25.5% POLYETHYLENE GLYCOL 4000 15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.15 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.599 α = 90 b = 46.689 β = 91.35 c = 141.198 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2010-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.1 49.01 96.9 0.09 11.02 2.7 49651 -3
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 2.1 2.23 93.4 0.44 3.35 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 2D3Q 2.1 49.03 47167 2483 100 0.18364 0.17966 0.181 0.26088 0.261 RANDOM 26.19
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] -0.15 -1.14 0.65 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.728 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 8.888 r_scangle_it 3.39 r_mcangle_it 3.197 r_scbond_it 2.588 r_mcbond_it 2.242 r_angle_refined_deg 1.247 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.728 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 8.888 r_scangle_it 3.39 r_mcangle_it 3.197 r_scbond_it 2.588 r_mcbond_it 2.242 r_angle_refined_deg 1.247 r_chiral_restr 0.102 r_gen_planes_refined 0.015 r_bond_refined_d 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 6636 Nucleic Acid Atoms Solvent Atoms 679 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing