7PTZ

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PQR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	0.1 M citric acid pH 3.5 and 3.0 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.63

Crystal Data

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

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2021-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.09	48.5	91.3	0.059	0.99	19.3	11.99		96541

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.16			0.73

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7PQR	1.093	48.5	96076	4828	91.614	0.124	0.1235	0.1393	17.228

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]
0.445			0.445		-0.891

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.202
r_dihedral_angle_4_deg	18.481
r_dihedral_angle_3_deg	9.173
r_dihedral_angle_1_deg	6.835
r_rigid_bond_restr	6.045
r_lrange_it	3.441
r_lrange_other	3.305
r_scbond_it	3.121
r_scbond_other	3.103
r_mcangle_other	2.88
r_scangle_it	2.831
r_mcangle_it	2.814
r_scangle_other	2.795
r_mcbond_it	2.426
r_mcbond_other	2.287
r_angle_refined_deg	2.032
r_angle_other_deg	1.662
r_nbd_other	0.288
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.234
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.139
r_metal_ion_refined	0.111
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing