6SHM

An inactive (D136A and D137A) variant of alpha-1,6-mannanase, GH76A of Salegentibacter sp. HEL1_6 in complex with alpha-1,6-mannotetrose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	1.6 M Tri-sodium citrate 10 % Glycerol 0.1 M MES monohydrate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.15	α = 90
b = 85.31	β = 90
c = 95.03	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	DECTRIS PILATUS 6M-F		2019-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03320	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.9	63.48	99.2	5.441	0.5969	2.333	0.279	7.3	9.3		24400

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	97.8		0.13602	15.103	6.236	0.241		7

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	6SHD	1.9	47.51	23304	1271	99.95	0.1208	0.1181	0.1722	RANDOM	12.801

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]
0.03			-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.083
r_dihedral_angle_4_deg	22.576
r_dihedral_angle_3_deg	14.241
r_dihedral_angle_1_deg	5.617
r_rigid_bond_restr	3.12
r_angle_refined_deg	1.706
r_angle_other_deg	1.66
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.083
r_dihedral_angle_4_deg	22.576
r_dihedral_angle_3_deg	14.241
r_dihedral_angle_1_deg	5.617
r_rigid_bond_restr	3.12
r_angle_refined_deg	1.706
r_angle_other_deg	1.66
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2689
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	63

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

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.