Experiment: 5UR6

PYR1 bound to the rationally designed agonist cyanabactin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UR4	PYR1 (PDB ID 5UR4)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	302	0.1 M Bis-tris propane, 2 M ammonium sulphate. Cryoprotected in perfluoropolyether cryo-oil

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.436	α = 90
b = 88.222	β = 90
c = 112.072	γ = 90

Symmetry
Space Group	F 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2016-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.63	50	99.1	0.052	0.057	0.022	63	6.7		25599			19.79

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66	100		0.117	0.127	0.049	0.987		6.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PYR1 (PDB ID 5UR4)	1.631	34.66	25499	2006	98.55	0.1894	0.1869	0.1869	0.2188	0.2195	Random	27.9941

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.586
f_angle_d	0.813
f_chiral_restr	0.057
f_plane_restr	0.006
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1394
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	58

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL	data reduction
HKL	data scaling