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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 5 298 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 14% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.199 α = 90 b = 63.199 β = 90 c = 99.237 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 2003-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.891976 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.03 80 97.6 0.108 0.097 11.95 3.98 191427 186809 -3 -3 11.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.03 1.15 91.8 0.299 0.254 4.57 3.6 53827
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 1.04 44.688 176589 175971 9281 99.65 0.1151 0.11151 0.11092 0.1113 0.12301 0.1233 RANDOM 12.107
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_4_deg 19.816 r_dihedral_angle_3_deg 11.481 r_sphericity_free 10.469 r_dihedral_angle_1_deg 6.02 r_sphericity_bonded 5.034 r_scangle_it 4.054 r_scbond_it 3.051 r_mcangle_it 2.894 r_mcbond_it 2.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.517 r_dihedral_angle_4_deg 19.816 r_dihedral_angle_3_deg 11.481 r_sphericity_free 10.469 r_dihedral_angle_1_deg 6.02 r_sphericity_bonded 5.034 r_scangle_it 4.054 r_scbond_it 3.051 r_mcangle_it 2.894 r_mcbond_it 2.106 r_rigid_bond_restr 1.915 r_mcbond_other 1.585 r_angle_refined_deg 1.469 r_angle_other_deg 0.773 r_symmetry_vdw_other 0.307 r_nbd_refined 0.234 r_nbd_other 0.222 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.098 r_nbtor_other 0.092 r_symmetry_metal_ion_refined 0.073 r_metal_ion_refined 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 63
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling