7Q30 | pdb_00007q30

Mutant T91A of uridine phosphorylase from Shewanella oneidensis

X-RAY DIFFRACTION

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	PEG 8000, 1 M lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.66	α = 90
b = 91.66	β = 90
c = 47.56	γ = 120

Symmetry
Space Group	P 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		2016-05-27	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	1.9	30	99.4	1	15.6	6.38		35104

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	1.9	2.02			0.87

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	1.901	26.474	35104	1696	99.801	0.159	0.1565	0.16	0.2108	0.21	25.321

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]
-1.258	-0.629		-1.258		4.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.132
r_dihedral_angle_4_deg	19.624
r_dihedral_angle_3_deg	15.936
r_lrange_it	8.277
r_dihedral_angle_1_deg	7.13
r_scangle_it	7.075
r_scbond_it	5.253
r_mcangle_it	4.013
r_mcbond_it	3.024
r_angle_refined_deg	2.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.132
r_dihedral_angle_4_deg	19.624
r_dihedral_angle_3_deg	15.936
r_lrange_it	8.277
r_dihedral_angle_1_deg	7.13
r_scangle_it	7.075
r_scbond_it	5.253
r_mcangle_it	4.013
r_mcbond_it	3.024
r_angle_refined_deg	2.425
r_symmetry_nbd_refined	0.352
r_nbtor_refined	0.321
r_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.209
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.157
r_bond_refined_d	0.016
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3575
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	55

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.