3WXP | pdb_00003wxp

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	303	0.14M CHES, 0.5M potassium sodium tartrate, 0.15M lithium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.738	α = 90
b = 119.281	β = 90
c = 46.794	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 MX300HE		2014-07-17	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	1.42	50	99.5	0.055	16.6	6.5		62399

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	1.42	1.44	94.3		0.376		5.6	2870

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	1.42	46.84	62347	3157	99.67	0.1138	0.1118	0.11	0.1516	0.15	RANDOM	18.578

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]
1.36			0.81		-2.18

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	48.175
r_dihedral_angle_2_deg	36.624
r_sphericity_bonded	18.496
r_dihedral_angle_4_deg	18.368
r_dihedral_angle_3_deg	11.687
r_rigid_bond_restr	7.094
r_dihedral_angle_1_deg	7.055
r_angle_refined_deg	2.134
r_chiral_restr	0.192
r_bond_refined_d	0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	48.175
r_dihedral_angle_2_deg	36.624
r_sphericity_bonded	18.496
r_dihedral_angle_4_deg	18.368
r_dihedral_angle_3_deg	11.687
r_rigid_bond_restr	7.094
r_dihedral_angle_1_deg	7.055
r_angle_refined_deg	2.134
r_chiral_restr	0.192
r_bond_refined_d	0.021
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	87

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.