6ZDL | pdb_00006zdl

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG 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	6ZDK

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
2.58	52.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.864	α = 90
b = 127.864	β = 90
c = 48.809	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		2018-02-05	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	1.9	31.97	100	0.203	0.209	0.05	0.998	10.5	17.6		36208			30.3

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	99.8		3.43	3.534	0.843	0.546	1	17.4

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	6ZDK	1.9	31.97	36184	1779	99.89	0.194	0.1927	0.21	0.2234	0.23	29.729

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]
-1.009	-0.505		-1.009		3.273

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.506
r_dihedral_angle_4_deg	16.361
r_dihedral_angle_3_deg	14.233
r_dihedral_angle_1_deg	6.008
r_lrange_it	4.321
r_lrange_other	4.299
r_scangle_it	4.283
r_scangle_other	4.283
r_scbond_it	3.238
r_scbond_other	3.238
r_angle_other_deg	2.455
r_mcangle_it	2.273
r_mcangle_other	2.273
r_angle_refined_deg	2.073
r_mcbond_it	1.477
r_mcbond_other	1.476
r_symmetry_nbd_refined	0.348
r_nbd_other	0.278
r_nbd_refined	0.198
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.178
r_chiral_restr	0.133
r_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.035
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2938
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	130

Software

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