6ZFQ | pdb_00006zfq

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with bis-tris

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	100 mM bis-tris pH 5.5, 25% w/v PEG 3350. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.23 mM GlcIFG and 2.23 mM alpha-1,2-mannobiose (10 x molar ratio). 300 nl droplet (150 nl protein solution, 150 nl reservoir solution). The ligand additives are probably not required for crystallization.

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.812	α = 90
b = 106.994	β = 110.315
c = 43.884	γ = 90

Symmetry
Space Group	P 1 21 1

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		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97718	Diamond	I24

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	1.2	38.41	99.4	0.049	0.057	0.028	0.999	10.6	3.8		114498			12.49

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	1.2	1.22	94.7		0.695	0.854	0.485	0.804	1.5	2.8

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	6ZFN	1.2	38.41	114455	5555	99.308	0.143	0.1409	0.14	0.1812	0.19	23.781

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]
-3.612		1.62	-0.784		2.508

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.039
r_rigid_bond_restr	16.007
r_dihedral_angle_4_deg	14.289
r_dihedral_angle_3_deg	12.655
r_dihedral_angle_1_deg	6.338
r_lrange_it	5.054
r_lrange_other	4.832
r_scangle_it	4.778
r_scangle_other	4.777
r_scbond_it	4.048
r_scbond_other	4.047
r_mcangle_other	3.811
r_mcangle_it	3.759
r_mcbond_it	3.271
r_mcbond_other	3.233
r_angle_other_deg	2.353
r_angle_refined_deg	1.82
r_symmetry_xyhbond_nbd_other	0.242
r_nbd_other	0.22
r_nbd_refined	0.218
r_symmetry_nbd_other	0.212
r_symmetry_nbd_refined	0.198
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.134
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.089
r_bond_other_d	0.034
r_gen_planes_other	0.025
r_gen_planes_refined	0.014
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2865
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	14

Software

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