7Q31 | pdb_00007q31

Mutant D24G of uridine phosphorylase from E. coli

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 sulfate, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.1	α = 90
b = 150.1	β = 90
c = 50.06	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	PIXEL	DECTRIS PILATUS 6M		2018-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9537	ESRF	MASSIF-1

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	1.75	30	97.2	0.89	11.1	2.6		41245

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	1.75	1.8			0.67

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	1.75	30	41244	2187	97.216	0.166	0.163	0.16	0.2185	0.22	29.153

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]
-0.403	-0.202		-0.403		1.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.526
r_dihedral_angle_4_deg	20.07
r_dihedral_angle_3_deg	16.369
r_dihedral_angle_1_deg	7.012
r_lrange_it	6.218
r_scangle_it	5.99
r_scbond_it	4.744
r_mcangle_it	3.524
r_mcbond_it	3.005
r_angle_refined_deg	2.226
r_nbtor_refined	0.315
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.181
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.134
r_metal_ion_refined	0.052
r_bond_refined_d	0.015
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3752
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	27

Software

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