6ZFN | pdb_00006zfn

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	279	100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.752	α = 90
b = 81.68	β = 92.934
c = 52.994	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		2018-01-20	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	1.1	52.92	97.6	0.054	0.061	0.029	0.998	11.9	3.7		143298			8.98

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	1.1	1.12	71.3		0.223	0.271	0.15	0.944	3.3	2.6

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	6ZDF	1.1	52.92	143263	7225	97.529	0.107	0.1063	0.11	0.1279	0.13	14.999

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]
-0.257		-0.173	0.472		-0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.659
r_dihedral_angle_3_deg	12.836
r_dihedral_angle_4_deg	11.791
r_rigid_bond_restr	11.682
r_dihedral_angle_1_deg	11.196
r_lrange_it	3.474
r_lrange_other	3.472
r_scangle_it	2.554
r_scangle_other	2.554
r_angle_other_deg	2.503
r_mcangle_it	2.319
r_mcangle_other	2.318
r_angle_refined_deg	2.077
r_scbond_it	1.974
r_scbond_other	1.974
r_mcbond_other	1.705
r_mcbond_it	1.704
r_symmetry_nbd_refined	0.283
r_nbd_other	0.236
r_nbd_refined	0.234
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.172
r_chiral_restr	0.158
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.033
r_bond_refined_d	0.018
r_gen_planes_other	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2922
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	29

Software

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