6ZJ1 | pdb_00006zj1

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with tetrasaccharide N-glycan fragment 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	6ZFA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.414	α = 90
b = 129.414	β = 90
c = 50.201	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 EIGER2 XE 16M		2019-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95004	Diamond	I04

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	1.957	112.076	50.1	0.093	0.098	0.029	0.999	15.7	11.7		17490

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	1.957	2.155	11.9		1.448	1.522	0.463	0.658	1.6	10.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ZFA	1.957	64.707	17488	844	50.122	0.187	0.1838	0.19	0.2524	0.26	40.367

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]
-0.063	-0.032		-0.063		0.205

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.769
r_dihedral_angle_3_deg	15.956
r_dihedral_angle_4_deg	13.486
r_dihedral_angle_1_deg	7.275
r_lrange_it	7.177
r_lrange_other	7.166
r_scangle_it	5.298
r_scangle_other	5.297
r_mcangle_other	4.767
r_mcangle_it	4.758
r_scbond_it	3.839
r_scbond_other	3.839
r_mcbond_it	3.259
r_mcbond_other	3.229
r_angle_refined_deg	1.76
r_angle_other_deg	1.211
r_symmetry_xyhbond_nbd_refined	0.321
r_nbd_other	0.209
r_nbd_refined	0.207
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.176
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2992
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	109

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
STARANISO	data processing
REFMAC	phasing
XDS	data reduction