Experiment: 3HKK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UUH	PDB ENTRY 2uuh

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	2M AmSO4, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
5.9532	79.339

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.718	α = 90
b = 170.718	β = 90
c = 170.718	γ = 90

Symmetry
Space Group	F 2 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	CCD	MARMOSAIC 225 mm CCD		2009-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.9	98.564	99.9	0.145	0.145	4.856	25.1		9259			61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.9	3.06	100		0.855	0.855	0.9	25.4	1328

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2uuh	2.9	38.18	9214	440	99.98	0.187	0.187	0.185	0.232	RANDOM	46.433

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	32.705
r_dihedral_angle_4_deg	18.919
r_dihedral_angle_3_deg	18.227
r_dihedral_angle_1_deg	5.592
r_scangle_it	2.954
r_scbond_it	1.804
r_angle_refined_deg	1.582
r_mcangle_it	1.398
r_mcbond_it	0.761
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.705
r_dihedral_angle_4_deg	18.919
r_dihedral_angle_3_deg	18.227
r_dihedral_angle_1_deg	5.592
r_scangle_it	2.954
r_scbond_it	1.804
r_angle_refined_deg	1.582
r_mcangle_it	1.398
r_mcbond_it	0.761
r_nbtor_refined	0.313
r_nbd_refined	0.237
r_symmetry_hbond_refined	0.236
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.143
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1135
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	87

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PXSOFT	data collection
XSCALE	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.