Experiment: 5DOU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	0.4 M MgCl2, 0.2 M ammonium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.919	α = 90.66
b = 98.558	β = 98.65
c = 214.89	γ = 90.08

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2013-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97947	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.6	40	90.7	0.081	0.111	0.076	7.9	1.8	178654	178654

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	84.9		0.321	0.321	0.318	2.1	1.7	24542

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	MOLECULAR REPLACEMENT	THROUGHOUT	5DOT	2.6	40	169655	8988	90.7	0.1967	0.1949	0.2292	RANDOM	45.659

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]
0.17	-0.29	0.32	-2.92	-0.17	2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.256
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_3_deg	15.187
r_dihedral_angle_1_deg	5.903
r_mcangle_it	2.883
r_mcbond_it	1.759
r_mcbond_other	1.759
r_angle_refined_deg	1.404
r_angle_other_deg	0.948
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.256
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_3_deg	15.187
r_dihedral_angle_1_deg	5.903
r_mcangle_it	2.883
r_mcbond_it	1.759
r_mcbond_other	1.759
r_angle_refined_deg	1.404
r_angle_other_deg	0.948
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	44008
Nucleic Acid Atoms
Solvent Atoms	640
Heterogen Atoms	341

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
XSCALE	data reduction

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.