8B4G | pdb_00008b4g

Structure of a fungal LPMO bound to ligands

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.402	α = 90
b = 87.312	β = 104.812
c = 37.482	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS3 X 2M		2021-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.496	87.31	99.3	0.996	7.9	6.6		34235

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	1.5	1.52			0.509

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ZUD	1.496	43.656	34206	1711	99.211	0.15	0.1486	0.16	0.1809	0.19	14.843

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]
-0.706		0.398	0.004		0.432

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.374
r_dihedral_angle_4_deg	20.768
r_dihedral_angle_3_deg	11.843
r_dihedral_angle_1_deg	7.416
r_lrange_it	4.87
r_lrange_other	4.869
r_scangle_it	3.103
r_scangle_other	3.102
r_scbond_it	2.09
r_scbond_other	2.089
r_mcangle_it	1.854
r_angle_refined_deg	1.848
r_mcangle_other	1.838
r_dihedral_angle_other_2_deg	1.743
r_angle_other_deg	1.438
r_mcbond_it	1.246
r_mcbond_other	1.2
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.198
r_nbd_other	0.195
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.119
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.085
r_metal_ion_refined	0.063
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1724
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	33

Software

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