Experiment: 3D6P

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
2.17	43.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.239	α = 90
b = 32.823	β = 90.41
c = 72.466	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		2006-11-07	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	1.6	30		0.038	24	8.2	31	31526		-3	16.8

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	1.6	1.64	99.8		0.147	7.2	2.8	1573

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2G8Q	1.6	30	31015	29458	1557	98.39	0.18337	0.18153	0.18	0.21927	0.22	RANDOM	14.73

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]
-0.27		0.23	0.2		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.76
r_dihedral_angle_4_deg	12.546
r_dihedral_angle_3_deg	10.711
r_dihedral_angle_1_deg	5.731
r_scangle_it	2.663
r_scbond_it	1.693
r_angle_refined_deg	1.242
r_mcangle_it	1.099
r_mcbond_it	0.658
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.76
r_dihedral_angle_4_deg	12.546
r_dihedral_angle_3_deg	10.711
r_dihedral_angle_1_deg	5.731
r_scangle_it	2.663
r_scbond_it	1.693
r_angle_refined_deg	1.242
r_mcangle_it	1.099
r_mcbond_it	0.658
r_nbtor_refined	0.294
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	22

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.