3WY6 | pdb_00003wy6

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	303	0.12M CHES, 0.5M potassium sodium tartrate, 0.1M lithium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.03	α = 90
b = 118.865	β = 90
c = 46.873	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2012-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	50	95.6	0.07	11.2	3.7		55555

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	1.45	1.48	90.7		0.384		2.7	2565

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.45	41.55	55555	2790	95.35	0.1281	0.1255	0.13	0.1779	0.18	RANDOM	16.696

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]
0.77			-0.06		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	47.729
r_dihedral_angle_2_deg	37.824
r_dihedral_angle_4_deg	17.994
r_sphericity_bonded	16.998
r_dihedral_angle_3_deg	12.03
r_dihedral_angle_1_deg	7.17
r_rigid_bond_restr	6.158
r_angle_refined_deg	2.216
r_chiral_restr	0.174
r_bond_refined_d	0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	47.729
r_dihedral_angle_2_deg	37.824
r_dihedral_angle_4_deg	17.994
r_sphericity_bonded	16.998
r_dihedral_angle_3_deg	12.03
r_dihedral_angle_1_deg	7.17
r_rigid_bond_restr	6.158
r_angle_refined_deg	2.216
r_chiral_restr	0.174
r_bond_refined_d	0.024
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	137

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

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.