☰ Navigation Tabs
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, 17% PEG 10000, 200mM Zn-acetate, 100mM Na-cacodylate pH 6.5; Crystals were soaked with Mn2+; VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.645 α = 90 b = 63.645 β = 90 c = 99.598 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 120 IMAGE PLATE MAR scanner 345 mm plate 2002-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.800 ESRF BM1A
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 1.74 25 98.6 0.059 13.2 2.5 40092 40092 9.7
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) 1.74 1.78 99.4 0.297 2.8 2671
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 (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 1.78 24.71 36060 35577 1894 98.66 0.12675 0.1243 0.1283 0.17241 0.176 RANDOM 19.591
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.273 r_dihedral_angle_4_deg 17.825 r_dihedral_angle_3_deg 11.831 r_dihedral_angle_1_deg 6.291 r_scangle_it 4.166 r_mcangle_it 3.076 r_scbond_it 2.926 r_mcbond_it 2.205 r_angle_refined_deg 1.622 r_symmetry_hbond_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.273 r_dihedral_angle_4_deg 17.825 r_dihedral_angle_3_deg 11.831 r_dihedral_angle_1_deg 6.291 r_scangle_it 4.166 r_mcangle_it 3.076 r_scbond_it 2.926 r_mcbond_it 2.205 r_angle_refined_deg 1.622 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.318 r_metal_ion_refined 0.304 r_symmetry_vdw_refined 0.252 r_xyhbond_nbd_refined 0.215 r_nbd_refined 0.213 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.017 r_symmetry_metal_ion_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2431 Nucleic Acid Atoms Solvent Atoms 752 Heterogen Atoms 57
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling