7Q1J | pdb_00007q1j

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

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	34.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.59	α = 90
b = 150.59	β = 90
c = 46.29	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		2018-04-12	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	1.71	30	99.5	1	9.6	3.82		42058

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	1.71	1.75			0.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4R2X	1.71	30	42058	2149	99.451	0.208	0.2037	0.2	0.2808	0.28	26.903

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]
0.71	0.355		0.71		-2.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.046
r_dihedral_angle_4_deg	19.674
r_dihedral_angle_3_deg	17.174
r_dihedral_angle_1_deg	8.315
r_lrange_it	6.773
r_scangle_it	6.029
r_scbond_it	4.752
r_mcangle_it	4.667
r_mcbond_it	3.893
r_angle_refined_deg	2.609
r_nbtor_refined	0.315
r_metal_ion_refined	0.234
r_nbd_refined	0.232
r_symmetry_nbd_refined	0.221
r_chiral_restr	0.177
r_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.165
r_gen_planes_refined	0.019
r_bond_refined_d	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3766
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	27

Software

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