Experiment: 3TP1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.596	α = 90
b = 60.596	β = 90
c = 63.862	γ = 120

Symmetry
Space Group	P 63

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	MAR CCD 165 mm	BENT, VERTICALLY FOCUSING MIRROR	2005-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8034	EMBL/DESY, HAMBURG	X13

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	20	99.2	0.04	17	2.7	17501	17501		-3

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	1.68	99.8		0.32	3.2	2.2	2371

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	rigid body refinement	THROUGHOUT	PDB entry 2D4L	1.6	20	16534	16534	966	99.22	0.16866	0.16698	0.19733	RANDOM	31.095

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]
0.94	0.47		0.94		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.471
r_dihedral_angle_4_deg	24.465
r_dihedral_angle_1_deg	12.911
r_dihedral_angle_3_deg	11.885
r_scangle_it	7.401
r_scbond_it	5.358
r_mcangle_it	3.835
r_mcbond_it	2.908
r_angle_refined_deg	1.957
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.471
r_dihedral_angle_4_deg	24.465
r_dihedral_angle_1_deg	12.911
r_dihedral_angle_3_deg	11.885
r_scangle_it	7.401
r_scbond_it	5.358
r_mcangle_it	3.835
r_mcbond_it	2.908
r_angle_refined_deg	1.957
r_nbtor_refined	0.32
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.193
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.123
r_metal_ion_refined	0.082
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	823
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	29

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.