Experiment: 3D2F

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D2E	PDB ENTRY 3D2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	277	15 % (w/v) polyethyleneglycol-6000, 100 mM Tris-HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.5	α = 90
b = 141.902	β = 90
c = 151.68	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	MARRESEARCH		2007-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9780	SLS	X10SA

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	2.3	103.695	100	0.073	0.073	7.6	3.7		124395			45.99

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)
1	2.3	2.42	100		0.506	0.506	1.5	3.5	17980

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		THROUGHOUT	PDB ENTRY 3D2E	2.3	20	124106	6248	99.99	0.2	0.197	0.244	RANDOM	44.114

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]
0.1			-2.12		2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.301
r_dihedral_angle_4_deg	21.395
r_dihedral_angle_3_deg	18.073
r_dihedral_angle_1_deg	6.106
r_scangle_it	2.596
r_scbond_it	1.563
r_angle_refined_deg	1.43
r_mcangle_it	0.941
r_mcbond_it	0.494
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.301
r_dihedral_angle_4_deg	21.395
r_dihedral_angle_3_deg	18.073
r_dihedral_angle_1_deg	6.106
r_scangle_it	2.596
r_scbond_it	1.563
r_angle_refined_deg	1.43
r_mcangle_it	0.941
r_mcbond_it	0.494
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.23
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_metal_ion_refined	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15391
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	76

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.