Experiment: 5DF1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.94	α = 90
b = 95.47	β = 90
c = 172.21	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS 6M		2015-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.75	66.22	99.6	0.115	0.05	0.995	9.7	6.5		76022			29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	98.1		1.681	0.702	0.543	1.2	6.6	5501

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	5DCU	1.75	66.22	72135	3887	99.55	0.1882	0.1868	0.2153	RANDOM	34.4

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]
0.74			1.97		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	16.505
r_dihedral_angle_3_deg	11.744
r_dihedral_angle_1_deg	6.041
r_mcangle_it	2.21
r_mcbond_it	1.563
r_mcbond_other	1.563
r_angle_refined_deg	1.371
r_angle_other_deg	1.052
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	16.505
r_dihedral_angle_3_deg	11.744
r_dihedral_angle_1_deg	6.041
r_mcangle_it	2.21
r_mcbond_it	1.563
r_mcbond_other	1.563
r_angle_refined_deg	1.371
r_angle_other_deg	1.052
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5736
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms	145

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.