Experiment: 3E8J

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QT8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1 M ammonium acetate (not pH'ed), 0.1 M bis-tris (pH 5.5), 21% PEG 10K, 5 mM DTT; cryoprotected with 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.097	α = 90
b = 73.147	β = 90
c = 184.745	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2008-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.9795	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.27	50	97	0.057		6.7		34890		1	38.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.35	87.1		0.263		6.7	3092

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2qt8	2.27	50	34744	1735	96.68	0.191	0.188	0.245	RANDOM	27.895

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]
3.54			-0.65		-2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.81
r_dihedral_angle_3_deg	14.035
r_dihedral_angle_4_deg	12.86
r_dihedral_angle_1_deg	5.094
r_scangle_it	3.743
r_scbond_it	2.571
r_mcangle_it	2.098
r_mcbond_it	1.272
r_angle_refined_deg	1.019
r_angle_other_deg	0.993

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.81
r_dihedral_angle_3_deg	14.035
r_dihedral_angle_4_deg	12.86
r_dihedral_angle_1_deg	5.094
r_scangle_it	3.743
r_scbond_it	2.571
r_mcangle_it	2.098
r_mcbond_it	1.272
r_angle_refined_deg	1.019
r_angle_other_deg	0.993
r_mcbond_other	0.349
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4654
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	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.