5N6U

Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	24% PEG400, 0.1 M Na-HEPES pH 7, 200 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.25	α = 90
b = 75.56	β = 92.52
c = 217.88	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	PIXEL	DECTRIS PILATUS 6M		2015-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.08	49.5	98.9	0.185	0.216	0.11	7.3	3.74		71693

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.08	3.14			1.762	2.083	1.093

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	2JE8	3.08	49.5	71693	3813	88.15	0.20637	0.20376	0.25483	RANDOM

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]
-45.63		7.1	68.52		-22.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.409
r_dihedral_angle_3_deg	18.292
r_dihedral_angle_4_deg	17.068
r_long_range_B_refined	14.368
r_long_range_B_other	14.368
r_mcangle_it	10.407
r_mcangle_other	10.407
r_scangle_other	10.126
r_dihedral_angle_1_deg	9.083
r_mcbond_it	6.727
r_mcbond_other	6.727
r_scbond_it	6.453
r_scbond_other	6.453
r_angle_refined_deg	1.771
r_angle_other_deg	1.476
r_chiral_restr	0.113
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27200
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling