8B6D

Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	292.15	sodium citrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.752	α = 90
b = 65.752	β = 90
c = 329.552	γ = 90

Symmetry
Space Group	P 43 21 2

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 EIGER X 16M		2017-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976300	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.1	82.53	100	0.09	0.093	0.024	1	29.1	26.4		43788

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	2.1	2.18			1.26	1.28	0.24	1	3.86	26.9

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	FREE R-VALUE	apo-TaGalU	2.1	82.524	43675	2094	99.918	0.177	0.1748	0.2209	43.301

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]
1.638			1.638		-3.277

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.89
r_dihedral_angle_3_deg	14.255
r_lrange_it	8.532
r_lrange_other	8.508
r_dihedral_angle_2_deg	8.227
r_dihedral_angle_1_deg	6.951
r_scangle_it	6.157
r_scangle_other	6.156
r_scbond_it	4.133
r_scbond_other	4.132
r_mcangle_it	4.127
r_mcangle_other	4.127
r_mcbond_it	2.963
r_mcbond_other	2.954
r_angle_refined_deg	1.855
r_angle_other_deg	0.576
r_nbd_refined	0.221
r_symmetry_nbd_other	0.196
r_nbd_other	0.188
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_xyhbond_nbd_other	0.11
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4404
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Aimless	data scaling
MOLREP	phasing