7QQG

Crystal structure of MYORG bound to 1-deoxygalactonojirimycin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F2H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	100 mM HEPES pH 7.0, 10% PEG MME5000, 5% tasimate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.113	α = 80.777
b = 78.882	β = 80.209
c = 176.221	γ = 62.641

Symmetry
Space Group	P 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 EIGER2 XE 16M		2020-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	2.43	69.75	98.3	0.073	0.103	0.073	0.995	8.4	3.5		127078

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	2.43	2.47			0.724	1.024	0.724	0.555	1.4	3.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2F2H	2.43	69.75	126937	6096	98.126	0.225	0.2239	0.2497	56.614

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]
-2.596	0.001	2.982	0.311	-1.895	2.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.366
r_dihedral_angle_4_deg	20.098
r_dihedral_angle_3_deg	15.865
r_dihedral_angle_1_deg	7.435
r_lrange_it	4.222
r_lrange_other	4.218
r_mcangle_it	1.804
r_mcangle_other	1.804
r_scangle_it	1.706
r_scangle_other	1.706
r_angle_refined_deg	1.428
r_angle_other_deg	1.166
r_mcbond_it	1.1
r_mcbond_other	1.1
r_scbond_it	1.042
r_scbond_other	1.041
r_symmetry_xyhbond_nbd_refined	0.28
r_nbd_other	0.209
r_nbd_refined	0.191
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_other	0.172
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.096
r_ncsr_local_group_5	0.078
r_ncsr_local_group_1	0.076
r_ncsr_local_group_4	0.075
r_symmetry_nbtor_other	0.074
r_ncsr_local_group_2	0.073
r_ncsr_local_group_6	0.071
r_ncsr_local_group_3	0.067
r_chiral_restr	0.061
r_symmetry_xyhbond_nbd_other	0.046
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	18863
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	404

Software

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