7Q1I | pdb_00007q1i

Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence glycerol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R2X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M Potassium citrate tribasic monohydrate, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.52	α = 90
b = 150.52	β = 90
c = 46.25	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2018-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.8025	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	30	97.9	1	7.9	2.24		50485

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69			0.6

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	4R2X	1.65	30	46523	2353	98.947	0.181	0.1788	0.18	0.2293	0.23	19.565

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]
0.237	0.118		0.237		-0.768

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.811
r_dihedral_angle_4_deg	22.782
r_dihedral_angle_3_deg	14.63
r_dihedral_angle_1_deg	7.372
r_lrange_it	4.771
r_scangle_it	4.41
r_scbond_it	3.304
r_mcangle_it	2.604
r_angle_refined_deg	2.352
r_mcbond_it	2.165
r_nbtor_refined	0.305
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.18
r_chiral_restr	0.147
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.129
r_metal_ion_refined	0.065
r_bond_refined_d	0.018
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3766
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	51

Software

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