4MIF

Pyranose 2-oxidase from Phanerochaete chrysosporium, wild type from natural source


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PL8pdb entry 3PL8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22980.1 M MES, 0.2 M MgCl2, 32% (w/v) PEG 400, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2562.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.034α = 90
b = 164.034β = 90
c = 232.521γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0000MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.847.4399.917.111.1331914331914
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.92.111.249157

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3PL81.846.4329915329915199999.90.152730.152610.171RANDOM29.711
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]
-0.07-0.04-0.070.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg19.56
r_dihedral_angle_3_deg13.471
r_dihedral_angle_1_deg6.719
r_angle_refined_deg2.226
r_angle_other_deg1.115
r_chiral_restr0.212
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.242
r_dihedral_angle_4_deg19.56
r_dihedral_angle_3_deg13.471
r_dihedral_angle_1_deg6.719
r_angle_refined_deg2.226
r_angle_other_deg1.115
r_chiral_restr0.212
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18148
Nucleic Acid Atoms
Solvent Atoms1562
Heterogen Atoms213

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling