7PU1

High resolution X-ray structure of Thermoascus aurantiacus LPMO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YET 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.653α = 90
b = 89.046β = 103.335
c = 70.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9538MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.0637.3484.20.0540.9918.576.6171807
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.061.10.440.893.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2YET1.0637.37163069875884.2440.1190.117350.1185112.983
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]
0.0720.194-0.2210.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.731
r_dihedral_angle_4_deg20.868
r_dihedral_angle_1_deg19.132
r_dihedral_angle_3_deg11.886
r_rigid_bond_restr8.906
r_lrange_it3.715
r_scbond_it3.625
r_scbond_other3.624
r_lrange_other3.271
r_scangle_it3.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.731
r_dihedral_angle_4_deg20.868
r_dihedral_angle_1_deg19.132
r_dihedral_angle_3_deg11.886
r_rigid_bond_restr8.906
r_lrange_it3.715
r_scbond_it3.625
r_scbond_other3.624
r_lrange_other3.271
r_scangle_it3.24
r_scangle_other3.24
r_angle_refined_deg2.304
r_mcangle_it1.834
r_mcangle_other1.82
r_angle_other_deg1.624
r_mcbond_it1.376
r_mcbond_other1.356
r_nbd_refined0.253
r_xyhbond_nbd_refined0.208
r_symmetry_nbd_other0.203
r_symmetry_xyhbond_nbd_refined0.179
r_nbtor_refined0.175
r_symmetry_nbd_refined0.142
r_chiral_restr0.129
r_nbd_other0.103
r_symmetry_nbtor_other0.1
r_metal_ion_refined0.091
r_bond_refined_d0.019
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_other_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3445
Nucleic Acid Atoms
Solvent Atoms719
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
TRUNCATEdata scaling
REFMACphasing