4MAI | pdb_00004mai

Structure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxygenase with Cu(I)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	292	10 mM zinc chloride, 100 mM MES, pH 6.0, 20% w/v PEG6000, crystals soaked in solution containing 2 mM copper chloride to replace zinc, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.269	α = 90
b = 60.629	β = 90
c = 65.176	γ = 90

Symmetry
Space Group	P 21 21 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		2013-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.980	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.4	44.39	99.3	0.052	0.033	17.9	6.3	44262	44262	1	1	11.7

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	1.4	1.42	95.7		0.742	2	5.1	2093

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	ISOTROPIC STRUCTURE REFINEMENT	THROUGHOUT	1.4	42.63	44262	42001	2200	99.07	0.1323	0.1323	0.1314	0.1306	0.1507	0.1493	RANDOM	18.6373

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]
-0.4			0.13		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.16
r_dihedral_angle_2_deg	30.329
r_dihedral_angle_4_deg	22.076
r_sphericity_bonded	10.715
r_dihedral_angle_3_deg	8.866
r_dihedral_angle_1_deg	7.003
r_mcangle_it	2.352
r_rigid_bond_restr	2.204
r_mcbond_it	1.81
r_mcbond_other	1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.16
r_dihedral_angle_2_deg	30.329
r_dihedral_angle_4_deg	22.076
r_sphericity_bonded	10.715
r_dihedral_angle_3_deg	8.866
r_dihedral_angle_1_deg	7.003
r_mcangle_it	2.352
r_rigid_bond_restr	2.204
r_mcbond_it	1.81
r_mcbond_other	1.81
r_angle_refined_deg	1.416
r_angle_other_deg	0.835
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1377
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	14

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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.