Experiment: 9DZS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		other solved exp. R699 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Protein/cofactor mix: 12mg/ml R699, 10mM MnCl2, 10mM UDP glucose, 50% glycerol. Mother liquor: 0.18 M Ammonium chloride, 18% (w/v) PEG 3350, 4% v/v 1-Propanol. The ratio of mix and mother liquor was at 1:1.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.041	α = 90
b = 71.481	β = 123.178
c = 72.626	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	DECTRIS EIGER X 16M		2022-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	60.79	99.3	0.083	0.998	10.9	6.9		349711

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	98.5		0.491	0.921	2.7	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	1.75	57.98	50656	2462	99.166	0.172	0.1706	0.1789	0.1953	0.2051	20.727

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]
3.44		-1.188	-0.387		-0.808

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.805
r_dihedral_angle_3_deg	12.17
r_dihedral_angle_1_deg	6.877
r_lrange_it	6.216
r_dihedral_angle_2_deg	6.079
r_scangle_it	4.593
r_mcangle_it	2.979
r_scbond_it	2.883
r_mcbond_it	1.892
r_angle_refined_deg	1.695

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.805
r_dihedral_angle_3_deg	12.17
r_dihedral_angle_1_deg	6.877
r_lrange_it	6.216
r_dihedral_angle_2_deg	6.079
r_scangle_it	4.593
r_mcangle_it	2.979
r_scbond_it	2.883
r_mcbond_it	1.892
r_angle_refined_deg	1.695
r_nbtor_refined	0.318
r_nbd_refined	0.201
r_symmetry_nbd_refined	0.194
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.149
r_chiral_restr	0.119
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3605
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DIALS	data collection
xia2	data reduction
Aimless	data scaling
PHENIX	phasing
PHASER	phasing
Coot	model building
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.