Experiment: 3IIJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RKB

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, 2 mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.144	α = 90
b = 99.144	β = 90
c = 57.838	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	2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.11665	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	1.76	30	98.1	0.044	17.92	4.9	32104	31610		2	32.8

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	1.76	1.79	88.4		0.499	3.41	4.3

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	1.76	28.3	2	31610	30007	1595	98.6	0.18193	0.18193	0.18121	0.19509	RANDOM	21.63

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.315
r_dihedral_angle_4_deg	18.765
r_dihedral_angle_3_deg	12.862
r_dihedral_angle_1_deg	4.685
r_scangle_it	2.393
r_scbond_it	1.448
r_angle_refined_deg	1.128
r_mcangle_it	0.876
r_mcbond_it	0.454
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.315
r_dihedral_angle_4_deg	18.765
r_dihedral_angle_3_deg	12.862
r_dihedral_angle_1_deg	4.685
r_scangle_it	2.393
r_scbond_it	1.448
r_angle_refined_deg	1.128
r_mcangle_it	0.876
r_mcbond_it	0.454
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1441
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	47

Software

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

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.