7Q2W

Mutant T91S of uridine phosphorylase from Shewanella oneidensis

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	0.1 M Bis-Tris, pH 6.5, 0.2 M ammonium sulfate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.4	α = 90
b = 95.49	β = 120.025
c = 91.41	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	CCD	MAR CCD 165 mm		2016-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.964	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	25	97	0.99	8.8	5.09		159146

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	1.75			0.88

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	4R2X	1.654	25	159145	7780	98.289	0.193	0.1909	0.2324	17.455

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]
-18.41		-8.14	32.512		-14.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	18.049
r_dihedral_angle_3_deg	15.799
r_dihedral_angle_1_deg	8.696
r_lrange_it	4.351
r_lrange_other	4.351
r_scangle_it	2.925
r_scangle_other	2.923
r_mcangle_it	2.916
r_mcangle_other	2.916
r_angle_refined_deg	2.315
r_scbond_it	2.197
r_scbond_other	2.194
r_mcbond_it	2.179
r_mcbond_other	2.178
r_angle_other_deg	1.537
r_xyhbond_nbd_refined	0.233
r_nbd_other	0.228
r_symmetry_xyhbond_nbd_refined	0.217
r_nbd_refined	0.214
r_xyhbond_nbd_other	0.212
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.116
r_symmetry_xyhbond_nbd_other	0.109
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.015
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10898
Nucleic Acid Atoms
Solvent Atoms	839
Heterogen Atoms	55

Software

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