6ZDK

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES and hexatungstotellurate(VI) TEW

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZDF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer.

Crystal Properties
Matthews coefficient	Solvent content
2.61	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.968	α = 90
b = 128.968	β = 90
c = 48.791	γ = 120

Symmetry
Space Group	P 62

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		2018-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2	64.48	99.6	0.126	0.149	0.078	0.992	6.2	3.5		31607

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	2	2.05	98.3		0.739	0.869	0.45	0.411	1.5	3.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ZDF	2	64.48	31481	1554	99.592	0.198	0.1956	0.235	32.842

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]
-1.779	-0.89		-1.779		5.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.789
r_dihedral_angle_4_deg	18.755
r_dihedral_angle_3_deg	15.88
r_dihedral_angle_1_deg	6.13
r_lrange_it	5.317
r_lrange_other	5.29
r_scangle_it	4.459
r_scangle_other	3.617
r_scbond_it	3.245
r_mcangle_other	2.798
r_mcangle_it	2.793
r_angle_other_deg	2.318
r_scbond_other	2.224
r_angle_refined_deg	1.963
r_mcbond_it	1.804
r_mcbond_other	1.775
r_nbd_other	0.266
r_symmetry_nbd_refined	0.232
r_symmetry_nbd_other	0.196
r_nbd_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.129
r_symmetry_nbtor_other	0.077
r_bond_other_d	0.035
r_metal_ion_refined	0.035
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2986
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	109

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing