6ZFA | pdb_00006zfa

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG, alpha-1,2-mannobiose 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
2.55	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.891	α = 90
b = 127.891	β = 90
c = 48.352	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	0.97622	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	1.8	110.76	100	0.148	0.153	0.038	0.999	13.4	16.5		42149			21.59

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	1.8	1.84	100		0.939	0.969	0.237	0.782	2.9	16.6

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	6ZDK	1.8	110.757	42104	2094	99.936	0.187	0.1855	0.2	0.2166	0.22	24.343

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]
-0.893	-0.447		-0.893		2.898

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.832
r_dihedral_angle_1_deg	19.834
r_dihedral_angle_4_deg	18.142
r_dihedral_angle_3_deg	13.767
r_lrange_it	5.036
r_lrange_other	5.018
r_scangle_it	4.06
r_scangle_other	4.059
r_scbond_it	3.09
r_scbond_other	3.09
r_angle_other_deg	2.732
r_mcangle_it	2.291
r_mcangle_other	2.291
r_angle_refined_deg	2.215
r_mcbond_it	1.519
r_mcbond_other	1.518
r_symmetry_nbd_refined	0.356
r_nbd_other	0.268
r_symmetry_nbd_other	0.204
r_nbd_refined	0.197
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.142
r_chiral_restr	0.137
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.092
r_bond_other_d	0.034
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2942
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	153

Software

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