Experiment: 1YOE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8F	YeiK PDB code 1Q8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	MPD, Sodium Acetate, ribose, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.466	α = 90
b = 84.062	β = 90
c = 112.483	γ = 90

Symmetry
Space Group	I 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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.78	25	97.8	0.116	26.2	12.5	34056	34056	-3	-3	18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.86	77.4		0.475	2.9		2669

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	YeiK PDB code 1Q8F	1.78	25	34056	34056	1086	97.8	0.1681	0.16811	0.16733	0.19276	RANDOM	17.623

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]
0.62			-0.79		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.275
r_scangle_it	4.618
r_scbond_it	2.862
r_mcangle_it	1.743
r_angle_refined_deg	1.305
r_mcbond_it	1
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.275
r_scangle_it	4.618
r_scbond_it	2.862
r_mcangle_it	1.743
r_angle_refined_deg	1.305
r_mcbond_it	1
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.072
r_metal_ion_refined	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2295
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.