3PZ9

Native structure of endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

X-RAY DIFFRACTION

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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
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.463	α = 90
b = 83.352	β = 90
c = 92.179	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		2010-04-09	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	1.42	40.33	98.4				80074		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	1.42	1.47	86

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	SIRAS	THROUGHOUT	1.42	40.33	79961	79961	4002	98.34	0.14714	0.14545	0.17849	RANDOM	17.845

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]
0.15			-0.45		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.34
r_sphericity_free	14.313
r_dihedral_angle_4_deg	13.777
r_dihedral_angle_3_deg	12.461
r_sphericity_bonded	8.425
r_scangle_it	6.321
r_dihedral_angle_1_deg	6.094
r_scbond_it	4.787
r_mcangle_it	3.72
r_rigid_bond_restr	3.011
r_mcbond_it	2.747
r_angle_refined_deg	2.229
r_chiral_restr	0.175
r_bond_refined_d	0.03
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2927
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SHELX	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing