7ZN6 | pdb_00007zn6

Crystal structure of laccase-like multicopper oxidase (LMCO) from Thermothelomyces thermophilus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Alphafold 2.0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M NH4Cl 18% w/v PEG 6000 0.1 M MES pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.855	α = 90
b = 74.855	β = 90
c = 118.948	γ = 90

Symmetry
Space Group	P 43

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 R 4M		2021-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.9	118.95	100	0.105	0.114	0.043	0.999	14.8	12.9		51534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			1.028	1.126	0.456	0.886		11.9

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	THROUGHOUT	Alphafold 2.0	1.9	74.967	51486	2567	99.996	0.153	0.1516	0.16	0.1847	0.19	35.061

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]
-1.867			-1.867		3.733

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.459
r_dihedral_angle_4_deg	22.054
r_dihedral_angle_3_deg	13.715
r_dihedral_angle_1_deg	8.025
r_lrange_it	5.532
r_lrange_other	5.481
r_scangle_it	2.98
r_scangle_other	2.98
r_mcangle_it	2.282
r_mcangle_other	2.282
r_scbond_it	1.89
r_scbond_other	1.89
r_angle_refined_deg	1.7
r_mcbond_it	1.437
r_mcbond_other	1.437
r_angle_other_deg	1.358
r_nbd_refined	0.198
r_nbd_other	0.194
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.109
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.076
r_metal_ion_refined	0.038
r_symmetry_xyhbond_nbd_other	0.014
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4523
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing