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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 1QPA PDB ENTRY 1QPA
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, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.683 α = 90 b = 62.683 β = 90 c = 98.217 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 MARMOSAIC 325 mm CCD 2001-11-14 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 1.81 40 96.1 0.056 11.9 2.4 34670 33318 1 1 20.3
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 1.81 1.84 98.6 0.392 1.1
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 1QPA 1.81 32.9 31531 31531 1667 96.11 0.15465 0.15217 0.1544 0.201 0.2016 RANDOM 25.889
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 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.504 r_dihedral_angle_4_deg 21.18 r_dihedral_angle_3_deg 13.652 r_dihedral_angle_1_deg 7.302 r_scangle_it 4.354 r_mcangle_it 3.344 r_scbond_it 3.188 r_mcbond_it 2.509 r_angle_refined_deg 1.442 r_symmetry_hbond_refined 0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.504 r_dihedral_angle_4_deg 21.18 r_dihedral_angle_3_deg 13.652 r_dihedral_angle_1_deg 7.302 r_scangle_it 4.354 r_mcangle_it 3.344 r_scbond_it 3.188 r_mcbond_it 2.509 r_angle_refined_deg 1.442 r_symmetry_hbond_refined 0.434 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.116 r_metal_ion_refined 0.112 r_symmetry_metal_ion_refined 0.049 r_gen_planes_refined 0.017 r_bond_refined_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2360 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 65
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling