6ZJ5 | pdb_00006zj5

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcDMJ 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
2.57	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.549	α = 90
b = 128.549	β = 90
c = 48.264	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		2019-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	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	2.269	111.327	51.9	0.276	0.295	0.103	0.989	5.3	8		11089

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	2.269	2.536	15.4		1.52	1.617	0.547	0.569		8.6

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	2.269	111.327	11089	545	51.903	0.192	0.1882	0.2	0.2559	0.26	29.85

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]
0.579	0.289		0.579		-1.878

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.659
r_dihedral_angle_3_deg	17.512
r_dihedral_angle_4_deg	14.734
r_dihedral_angle_1_deg	7.606
r_lrange_it	6.663
r_lrange_other	6.656
r_scangle_it	3.176
r_scangle_other	3.175
r_mcangle_it	2.928
r_mcangle_other	2.928
r_scbond_it	2.474
r_scbond_other	2.474
r_mcbond_it	1.774
r_mcbond_other	1.768
r_angle_refined_deg	1.531
r_angle_other_deg	1.126
r_symmetry_xyhbond_nbd_refined	0.338
r_symmetry_nbd_refined	0.262
r_nbd_other	0.254
r_nbd_refined	0.207
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.174
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.06
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2993
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	161

Software

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