5IJU | pdb_00005iju

Structure of an AA10 Lytic Polysaccharide Monooxygenase from Bacillus amyloliquefaciens with Cu(II) bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YOX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	292	0.1 M NaOAc pH 5.0, 20 % PEG-6000, 0.2 M CaCl2 Micro seeded using crystals grown in 0.1 M MMT pH 4.0, 25 % PEG-1500

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.779	α = 90
b = 73.482	β = 100.4
c = 75.457	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	100	PIXEL	DECTRIS PILATUS 6M-F		2015-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	37.11	99.8	0.142	0.985	5.3	3.3		41043			7.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	99.4		0.62	1.3	2.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2YOX	1.7	37.11	41020	2062	99.65	0.2249	0.2229	0.23	0.2635	0.27	RANDOM	9.4268

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]
0.26		-0.42	0.28		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.397
r_dihedral_angle_4_deg	15.785
r_dihedral_angle_3_deg	13.358
r_dihedral_angle_1_deg	6.979
r_angle_other_deg	3.766
r_angle_refined_deg	1.637
r_mcangle_it	1.118
r_mcbond_it	0.664
r_mcbond_other	0.664
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.397
r_dihedral_angle_4_deg	15.785
r_dihedral_angle_3_deg	13.358
r_dihedral_angle_1_deg	6.979
r_angle_other_deg	3.766
r_angle_refined_deg	1.637
r_mcangle_it	1.118
r_mcbond_it	0.664
r_mcbond_other	0.664
r_chiral_restr	0.095
r_gen_planes_other	0.018
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2782
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	11

Software

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