6KPN | pdb_00006kpn

Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris D154N/E156Q mutant in complex with fucosyl-N-acetylglucosamine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.6	277.15	0.1 M CHES-NaOH (pH 8.6) and 20 % PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.732	α = 90
b = 105.732	β = 90
c = 63.207	γ = 120

Symmetry
Space Group	P 65

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 2M-F		2018-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

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	2.1	45.78	99.9	0.141	0.996	8	5.1		23548

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	99.4		1.241	0.484	1.3	5.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	19.98	22360	1136	99.83	0.2002	0.1979	0.2038	0.2438	0.2498	RANDOM	40.472

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]
-0.02	-0.01		-0.02		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.404
r_dihedral_angle_3_deg	13.169
r_dihedral_angle_4_deg	11.553
r_dihedral_angle_1_deg	7.639
r_angle_refined_deg	1.613
r_angle_other_deg	1.354
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.404
r_dihedral_angle_3_deg	13.169
r_dihedral_angle_4_deg	11.553
r_dihedral_angle_1_deg	7.639
r_angle_refined_deg	1.613
r_angle_other_deg	1.354
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2274
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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.