Experiment: 4DUB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IJ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	300	0.1 M sodium cacadylate, pH 5.5, 0.14 M Ca(Ac)2, 14 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.912	α = 90
b = 153.578	β = 95.1
c = 61.098	γ = 90

Symmetry
Space Group	P 1 21 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		2010-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.000	SSRL	BL12-2

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	1.7	39.143	97.7	0.048	13.7	3.5	115485	115485

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	1.7	1.79	97.9		0.663	0.663	1.2	3.5	16887

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 (All)	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	2IJ2	1.7	38.58	115433	115433	5822	97.57	0.166	0.166	0.164	0.17	0.2036	0.21	RANDOM	22.4201

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]
-0.79		1.16	-1.57		2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.359
r_dihedral_angle_4_deg	14.606
r_dihedral_angle_3_deg	13.684
r_dihedral_angle_1_deg	6.562
r_scangle_it	5.203
r_scbond_it	3.425
r_mcangle_it	2.139
r_angle_refined_deg	2.094
r_mcbond_it	1.368
r_chiral_restr	0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.359
r_dihedral_angle_4_deg	14.606
r_dihedral_angle_3_deg	13.684
r_dihedral_angle_1_deg	6.562
r_scangle_it	5.203
r_scbond_it	3.425
r_mcangle_it	2.139
r_angle_refined_deg	2.094
r_mcbond_it	1.368
r_chiral_restr	0.164
r_bond_refined_d	0.028
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7293
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	108

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XSCALE	data scaling
MOLREP	phasing

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.