3PZI

Structure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with beta-D-glucose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.43	α = 90
b = 83.234	β = 90
c = 91.916	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	CCD	MARMOSAIC 225 mm CCD		2010-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4586	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.55	35.4	99.9				62462		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61	99.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	35.4	59210	59210	3160	99.81	0.14227	0.14012	0.1827	RANDOM	17.022

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]
0.12			-0.32		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.991
r_dihedral_angle_4_deg	16.684
r_sphericity_free	13.239
r_dihedral_angle_3_deg	12.621
r_sphericity_bonded	7.848
r_scangle_it	6.293
r_dihedral_angle_1_deg	6
r_scbond_it	4.681
r_mcangle_it	3.415
r_rigid_bond_restr	2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.991
r_dihedral_angle_4_deg	16.684
r_sphericity_free	13.239
r_dihedral_angle_3_deg	12.621
r_sphericity_bonded	7.848
r_scangle_it	6.293
r_dihedral_angle_1_deg	6
r_scbond_it	4.681
r_mcangle_it	3.415
r_rigid_bond_restr	2.9
r_mcbond_it	2.479
r_angle_refined_deg	2.073
r_chiral_restr	0.167
r_bond_refined_d	0.027
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2927
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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 R01GM133198.