Experiment: 3D8Y

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G8Q	PDB entry 2G8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	PEG 4000, SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.161	α = 90
b = 32.421	β = 90.9
c = 72.567	γ = 90

Symmetry
Space Group	C 1 2 1

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		2006-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.92	SRS	PX9.6

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	1.72	30	97.9	0.078	9.2	10.8	25226	24530		-3	19.5

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	1.7	1.76	96.7		0.47	3	3.1	1218

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2G8Q	1.72	30	23272	1258	97.24	0.19137	0.18926	0.2296	RANDOM	16.746

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]
-0.39		0.17	0.73		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.195
r_dihedral_angle_3_deg	11.593
r_dihedral_angle_4_deg	10.506
r_dihedral_angle_1_deg	5.862
r_scangle_it	2.498
r_scbond_it	1.572
r_angle_refined_deg	1.204
r_mcangle_it	0.948
r_mcbond_it	0.553
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.195
r_dihedral_angle_3_deg	11.593
r_dihedral_angle_4_deg	10.506
r_dihedral_angle_1_deg	5.862
r_scangle_it	2.498
r_scbond_it	1.572
r_angle_refined_deg	1.204
r_mcangle_it	0.948
r_mcbond_it	0.553
r_nbtor_refined	0.292
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1901
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	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.