8B31 | pdb_00008b31

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	292.15	Bis-Tris-Propane, PEG3350, KSCN, Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.086	α = 90
b = 78.593	β = 93.885
c = 89.788	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		2019-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.75	89.58	99.8	0.059	0.069	0.035	0.99	10.5	3.7		67139

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	1.75	1.78	99.7		0.866	1.025	0.541	0.651	1.3	3.5

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	3JUJ	1.75	48.022	67108	3270	99.761	0.198	0.196	0.21	0.2262	0.24	32.816

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]
2.122		-1.419	-0.948		-0.972

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	18.407
r_dihedral_angle_6_deg	16.866
r_dihedral_angle_3_deg	14.084
r_dihedral_angle_2_deg	10.216
r_lrange_it	7.073
r_lrange_other	6.959
r_dihedral_angle_1_deg	6.756
r_scangle_it	4.341
r_scangle_other	4.34
r_mcangle_it	3.06
r_mcangle_other	3.06
r_scbond_it	2.919
r_scbond_other	2.919
r_mcbond_it	2.113
r_mcbond_other	2.113
r_angle_refined_deg	1.649
r_angle_other_deg	0.639
r_metal_ion_refined	0.304
r_nbd_refined	0.208
r_nbd_other	0.176
r_symmetry_nbd_other	0.168
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.11
r_symmetry_xyhbond_nbd_refined	0.106
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.072
r_chiral_restr_other	0.049
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	92

Software

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