7T5D | pdb_00007t5d

Neutron structure of Neurospora crassa Lytic Polysaccharide Monooxygenase 9D (NcLPMO9D) ascorbate soak

NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TKH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	295	PEG 3350, HEPES

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.73	α = 90
b = 42.18	β = 99
c = 69.76	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	neutron	100	DIFFRACTOMETER	ORNL ANGER CAMERA		2018-11-15	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	14.791	91.16	0.1851	0.2148	0.956	7.15	3.2		14168			31.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	84.86		0.2737	0.3327	0.297	2.28	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TKH	2.4	14.791	2.34	14167	710	91.64	0.2325	0.2286	0.3088	Random selection	38.9543

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	17.5745
f_angle_d	0.6888
f_chiral_restr	0.0503
f_bond_d	0.0063
f_plane_restr	0.0041

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms
Solvent Atoms	1242
Heterogen Atoms	118

Software

Software
Software Name	Purpose
PHENIX	refinement
Mantid	data reduction
LaueView	data scaling
PHASER	phasing
Coot	model building

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.