Experiment: 4NOD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	12% PEG8000, 22% glycerol, 0.04 M potassium phosphate monobasic, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.372	α = 79.86
b = 82.49	β = 85.48
c = 104.222	γ = 84.53

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	Rh coated mirrors	2012-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.0332	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.897	39	50	0.038	13.5	2	40810	35526	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.897

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3TQ6	2.897	35.64	2	33743	1783	87.05	0.267	0.22345	0.22108	0.26744	RANDOM	99.732

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]
-2.88	-0.23	-0.16	2.59	5	0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_4_deg	19.822
r_dihedral_angle_3_deg	19.385
r_long_range_B_refined	15.691
r_mcangle_it	8.906
r_scbond_it	6.991
r_mcbond_it	5.71
r_dihedral_angle_1_deg	4.956
r_angle_refined_deg	1.391
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_4_deg	19.822
r_dihedral_angle_3_deg	19.385
r_long_range_B_refined	15.691
r_mcangle_it	8.906
r_scbond_it	6.991
r_mcbond_it	5.71
r_dihedral_angle_1_deg	4.956
r_angle_refined_deg	1.391
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6408
Nucleic Acid Atoms	3577
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.