3FM4

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FKGPDB ENTRY 3FKG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52989.0mg/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 coefficientSolvent content
2.7955.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.794α = 90
b = 62.794β = 90
c = 97.875γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2001-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8065EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.114097.60.0849.12.82201321485
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.1578.50.3671.7839

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FKG2.1132.882072420357109598.230.144180.144180.141260.19776RANDOM28.046
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]
-0.24-0.240.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.293
r_dihedral_angle_4_deg16.297
r_dihedral_angle_3_deg14.281
r_dihedral_angle_1_deg7.412
r_scangle_it3.998
r_mcangle_it3.341
r_scbond_it3.275
r_mcbond_it2.448
r_angle_refined_deg1.379
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.293
r_dihedral_angle_4_deg16.297
r_dihedral_angle_3_deg14.281
r_dihedral_angle_1_deg7.412
r_scangle_it3.998
r_mcangle_it3.341
r_scbond_it3.275
r_mcbond_it2.448
r_angle_refined_deg1.379
r_nbtor_refined0.317
r_nbd_refined0.228
r_symmetry_hbond_refined0.227
r_xyhbond_nbd_refined0.204
r_symmetry_vdw_refined0.201
r_metal_ion_refined0.149
r_chiral_restr0.106
r_gen_planes_refined0.015
r_bond_refined_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2353
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms63

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling