7T5E | pdb_00007t5e

Neutron structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) low pH vapor exchange

X-RAY DIFFRACTION - 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	4.4	295	PEG 3350, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.296	α = 90
b = 42.269	β = 98.47
c = 70.413	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	295	PIXEL	DECTRIS EIGER R 4M		2018-10-25	M	SINGLE WAVELENGTH
2	1	neutron	295	DIFFRACTOMETER	ORNL ANGER CAMERA		2018-07-17	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54
2	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2-4	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	12.65	97.56	0.1152		0.1258		0.991		15.24	6.1		30950			17.17
2	2.14	14.65	84.65	0.1532		0.1751		0.97		10.01	4		18963			17.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.9		0.299		0.3443		0.88		4.4	4.1
2	2.14	2.22		0.328		0.3824		0.363		3.02	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.9	12.662		1.34		30948	1557	97.96		0.1303	0.1275	0.13	0.182	0.18	Random selection	23.5275
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.144	14.649				18770	954	84.98		0.148	0.1444		0.2137		Random selection

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	21.0533
f_angle_d	1.3218
f_chiral_restr	0.0707
f_bond_d	0.0101
f_plane_restr	0.0071

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3271
Nucleic Acid Atoms
Solvent Atoms	1167
Heterogen Atoms	155

Software

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

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.