Experiment: 3IIL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1 M HEPES pH 7.5, 1.5 M Li2SO4, 0.2 M NaCl, 0.5 mM DTT, 25 mM MgCl2, 25 mM P1,P5-Di(Adenosine-5')Pentaphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.173	α = 90
b = 99.173	β = 90
c = 58.048	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 225 mm CCD	Rh Coated mirrors	2007-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.04498	SRS	PX10.1

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	2	34.52	99.9	0.057	20.13	6.5	22145	22102		2	32.9

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	2	2.03	100		0.461	4.25	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1RKB	2	34.52	2	22102	20968	1131	99.86	0.17211	0.17211	0.17099	0.19269	RANDOM	22.776

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
r_dihedral_angle_2_deg	38.786
r_dihedral_angle_3_deg	14.258
r_dihedral_angle_4_deg	7.893
r_dihedral_angle_1_deg	4.941
r_scangle_it	2.794
r_scbond_it	1.674
r_angle_refined_deg	1.258
r_mcangle_it	1.033
r_mcbond_it	0.543
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.786
r_dihedral_angle_3_deg	14.258
r_dihedral_angle_4_deg	7.893
r_dihedral_angle_1_deg	4.941
r_scangle_it	2.794
r_scbond_it	1.674
r_angle_refined_deg	1.258
r_mcangle_it	1.033
r_mcbond_it	0.543
r_chiral_restr	0.095
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1441
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	56

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.