Experiment: 5TDX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YB6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	1:1 mix of protein (in 5mM BES buffer) with mother liquor (1.1 Molar Ammonium Citrate, 50 mM bis-tris propane, pH 6.8) Crystals formed after 2-3 weeks at 20 degrees C. Crystals were cryo-protected in 5% glycerol in mother liquor for 10 seconds then flash frozen in LN2.

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.265	α = 90
b = 108.265	β = 90
c = 201.188	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2014-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.96	29.32	99.3	0.097	0.998	13.8	8.5		86348

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	1.99	88.3		0.68	0.772		5.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YB6	1.96	29.32	81902	4319	99.28	0.1792	0.1767	0.19	0.2265	0.23	RANDOM	38.133

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.483
r_dihedral_angle_3_deg	15.665
r_dihedral_angle_4_deg	14.161
r_dihedral_angle_1_deg	6.539
r_mcangle_it	2.789
r_angle_refined_deg	2.346
r_mcbond_it	1.991
r_mcbond_other	1.991
r_angle_other_deg	1.207
r_chiral_restr	0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.483
r_dihedral_angle_3_deg	15.665
r_dihedral_angle_4_deg	14.161
r_dihedral_angle_1_deg	6.539
r_mcangle_it	2.789
r_angle_refined_deg	2.346
r_mcbond_it	1.991
r_mcbond_other	1.991
r_angle_other_deg	1.207
r_chiral_restr	0.165
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8396
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	36

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data processing

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.