9D0Z | pdb_00009d0z

X-ray crystal structure of H157Q variant Thermothelomyces thermophilus polysaccharide monooxygenase 9E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9BJQ	WT MtPMO9E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	The crystal was grown by hanging drop in conditions optimized from Hampton Index HT G8 (0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25 % w/v polyethylene glycol 3,350). H157Q Mt PMO9E was first reconstituted with excess copper and buffer exchanged to buffer with 50 mM MOPS and 50 mM HEPES pH 6. 1 ul 30 mg/mL H157Q Mt PMO9E was then mixed with 1 uL with 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, and 26 % PEG 3,350 in a hanging drop. Crystals grew within 4 days. The crystal was looped with a 0.1-0.2 mm loop, then cryoprotected for 10 seconds in well solution mixed with cryoprotectants to a final concentration of 8% w/v sucrose, 2% w/v glucose, 8% v/v glycerol, and 8% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.41	α = 90
b = 122.473	β = 90
c = 91.478	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2023-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.000046	ALS	5.0.2

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	1.8	45.74	99.5	0.135	0.157	0.08	0.985	6	3.6		53154			18.67

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	1.8	1.84	99.7		0.537	0.627	0.377	0.811	2	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	44.68	1.33	52001	2016	97.21	0.2125	0.2115	0.2148	0.2363	0.2392	23.17

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.5002
f_angle_d	0.8484
f_chiral_restr	0.0554
f_plane_restr	0.0066
f_bond_d	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3420
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	22

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.