7ZJB | pdb_00007zjb

Structural and functional characterization of the bacterial lytic polysaccharide Monooxygenase ScLPMO10D


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IF7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52982.0 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.3262.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.08α = 90
b = 59.08β = 90
c = 145.718γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97702ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.3748.5799.80.05122.512.655188
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.4299.61.3690.7891.612.7

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 REPLACEMENTTHROUGHOUT6IF71.3754.8152497271299.490.130450.129340.130.152320.16RANDOM23.296
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]
0.090.09-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.878
r_dihedral_angle_1_deg19.067
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg11.759
r_long_range_B_refined9.619
r_rigid_bond_restr5.253
r_scbond_it5.165
r_long_range_B_other4.319
r_scangle_other4.277
r_scbond_other4.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1351
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing