7PTZ

High resolution X-ray structure of E. coli expressed Lentinus similis LPMO.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PQR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.52930.1 M citric acid pH 3.5 and 3.0 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.5952.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.659α = 90
b = 48.659β = 90
c = 109.593γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9763MAX 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
11.0948.591.30.0590.9919.311.9996541
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.091.160.73

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-VALUE7PQR1.09348.596076482891.6140.1240.12350.139317.228
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]
0.4450.445-0.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.202
r_dihedral_angle_4_deg18.481
r_dihedral_angle_3_deg9.173
r_dihedral_angle_1_deg6.835
r_rigid_bond_restr6.045
r_lrange_it3.441
r_lrange_other3.305
r_scbond_it3.121
r_scbond_other3.103
r_mcangle_other2.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.202
r_dihedral_angle_4_deg18.481
r_dihedral_angle_3_deg9.173
r_dihedral_angle_1_deg6.835
r_rigid_bond_restr6.045
r_lrange_it3.441
r_lrange_other3.305
r_scbond_it3.121
r_scbond_other3.103
r_mcangle_other2.88
r_scangle_it2.831
r_mcangle_it2.814
r_scangle_other2.795
r_mcbond_it2.426
r_mcbond_other2.287
r_angle_refined_deg2.032
r_angle_other_deg1.662
r_nbd_other0.288
r_symmetry_nbd_refined0.252
r_nbd_refined0.234
r_symmetry_xyhbond_nbd_refined0.217
r_symmetry_nbd_other0.197
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.178
r_chiral_restr0.139
r_metal_ion_refined0.111
r_symmetry_nbtor_other0.09
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1787
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing