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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 5.9 298 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 16% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.333 α = 90 b = 63.333 β = 90 c = 99.226 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 2002-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97992 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 1.13 40 99.9 0.085 0.096 13.5 4.1 145501 145501 -3 -3 11.9
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 1.13 1.16 99.8 0.13 0.156 7 3.13 145501
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 1.13 28.323 138344 138206 7291 99.9 0.1004 0.1004 0.09965 0.1009 0.11482 0.1154 RANDOM 10.768
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] 0.08 0.08 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 21.501 r_dihedral_angle_3_deg 11.199 r_sphericity_free 10.29 r_dihedral_angle_1_deg 6.174 r_sphericity_bonded 4.88 r_scangle_it 3.791 r_scbond_it 2.795 r_mcangle_it 2.695 r_mcbond_it 1.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.067 r_dihedral_angle_4_deg 21.501 r_dihedral_angle_3_deg 11.199 r_sphericity_free 10.29 r_dihedral_angle_1_deg 6.174 r_sphericity_bonded 4.88 r_scangle_it 3.791 r_scbond_it 2.795 r_mcangle_it 2.695 r_mcbond_it 1.963 r_rigid_bond_restr 1.824 r_mcbond_other 1.647 r_angle_refined_deg 1.409 r_angle_other_deg 0.78 r_symmetry_vdw_other 0.292 r_symmetry_vdw_refined 0.291 r_nbd_other 0.245 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.183 r_metal_ion_refined 0.138 r_chiral_restr 0.094 r_nbtor_other 0.093 r_symmetry_metal_ion_refined 0.072 r_bond_refined_d 0.011 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 2354 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 67
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling