9FDL | pdb_00009fdl

Crystal structure of the catalytic domain of an AA9 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus (TtLPMO9F)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D7V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M of sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.891	α = 90
b = 112.293	β = 90
c = 262.381	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 EIGER X 16M		2023-12-08	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	2.33	262.38	100	0.324	0.35	0.132	0.993	6.5	13.4		35897

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	2.33	2.41			2.476	2.569	0.681	0.534		14.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.33	131.536	35828	1755	99.922	0.164	0.1623	0.1691	0.2041	0.2058	44.215

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]
-0.215			-0.786		1.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.689
r_dihedral_angle_3_deg	13.004
r_lrange_it	7.524
r_dihedral_angle_1_deg	7.485
r_lrange_other	7.446
r_dihedral_angle_2_deg	6.454
r_scangle_it	5.92
r_scangle_other	5.92
r_mcangle_it	4.544
r_mcangle_other	4.544
r_scbond_it	4.173
r_scbond_other	4.172
r_mcbond_it	3.329
r_mcbond_other	3.329
r_angle_refined_deg	1.857
r_angle_other_deg	0.627
r_symmetry_nbd_other	0.21
r_nbd_refined	0.204
r_nbtor_refined	0.182
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.171
r_symmetry_nbd_refined	0.114
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.087
r_ncsr_local_group_2	0.087
r_ncsr_local_group_3	0.085
r_ncsr_local_group_1	0.08
r_symmetry_xyhbond_nbd_other	0.035
r_bond_refined_d	0.011
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	5085
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	30

Software

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