4B5Q

The lytic polysaccharide monooxygenase GH61D structure from the basidiomycota fungus Phanerochaete chrysosporium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EIIPDB ENTRY 3EII

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP712MG/ML PROTEIN, WITH EQUAL VOLUME 2.1 M DL-MALIC ACID PH 7.0 USING SITTING DROP CRYSTALLIZATION
Crystal Properties
Matthews coefficientSolvent content
1.9938.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.308α = 90
b = 37.521β = 117.41
c = 79.848γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7540.0798.50.0910.93.4394202
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8497.50.562.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3EII1.7570.8837442197798.110.187580.18570.190.22290.22RANDOM17.353
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]
-0.69-0.361.27-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.783
r_dihedral_angle_4_deg19.723
r_dihedral_angle_3_deg12.412
r_dihedral_angle_1_deg6.182
r_angle_refined_deg1.165
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3328
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing