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Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FKG PDB ENTRY 3FKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 16% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.794 α = 90 b = 62.794 β = 90 c = 97.875 γ = 90
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 MAR CCD 165 mm 2001-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8065 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.11 40 97.6 0.084 9.1 2.8 22013 21485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.15 78.5 0.367 1.7 839
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3FKG 2.11 32.88 20724 20357 1095 98.23 0.14418 0.14418 0.14126 0.1434 0.19776 0.1984 RANDOM 28.046
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.293 r_dihedral_angle_4_deg 16.297 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 7.412 r_scangle_it 3.998 r_mcangle_it 3.341 r_scbond_it 3.275 r_mcbond_it 2.448 r_angle_refined_deg 1.379 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.293 r_dihedral_angle_4_deg 16.297 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 7.412 r_scangle_it 3.998 r_mcangle_it 3.341 r_scbond_it 3.275 r_mcbond_it 2.448 r_angle_refined_deg 1.379 r_nbtor_refined 0.317 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_refined 0.201 r_metal_ion_refined 0.149 r_chiral_restr 0.106 r_gen_planes_refined 0.015 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2353 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 63
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling