3PZM

Structure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with three glycerol molecules

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	48.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.458	α = 90
b = 83.28	β = 90
c = 91.96	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	1.5	41.3	100			131640	68874		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	1.5	1.55	99.9

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	1.5	41.3	65092	65092	3474	99.58	0.1334	0.13121	0.17464	RANDOM	15.322

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]
0.17			-0.44		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.898
r_dihedral_angle_4_deg	15.839
r_sphericity_free	12.506
r_dihedral_angle_3_deg	11.583
r_sphericity_bonded	7.454
r_scangle_it	6.062
r_dihedral_angle_1_deg	6.05
r_scbond_it	4.559
r_mcangle_it	3.381
r_rigid_bond_restr	2.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.898
r_dihedral_angle_4_deg	15.839
r_sphericity_free	12.506
r_dihedral_angle_3_deg	11.583
r_sphericity_bonded	7.454
r_scangle_it	6.062
r_dihedral_angle_1_deg	6.05
r_scbond_it	4.559
r_mcangle_it	3.381
r_rigid_bond_restr	2.736
r_mcbond_it	2.475
r_angle_refined_deg	2.126
r_chiral_restr	0.166
r_bond_refined_d	0.026
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2927
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	26

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 National Science Foundation (DBI-1832184), 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.