Experiment: 4DN3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	4.3 M SODIUM FORMATE CRYO VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.17	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.54	α = 90
b = 121.54	β = 90
c = 84.23	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944	MIRRORS	2006-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.6	30	99.8	0.069		7.5	18826	18826		-3	39.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	98.4		0.455		7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	15	17765	17765	965	94.8	0.19364	0.19364	0.19057	0.24912	RANDOM	50.9

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]
-1.21			-1.21		2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	44.528
r_scangle_it	39.058
r_dihedral_angle_2_deg	37.638
r_dihedral_angle_3_deg	16.488
r_dihedral_angle_4_deg	11.648
r_dihedral_angle_1_deg	6.566
r_mcangle_it	5.318
r_mcbond_it	2.76
r_angle_refined_deg	1.304
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	44.528
r_scangle_it	39.058
r_dihedral_angle_2_deg	37.638
r_dihedral_angle_3_deg	16.488
r_dihedral_angle_4_deg	11.648
r_dihedral_angle_1_deg	6.566
r_mcangle_it	5.318
r_mcbond_it	2.76
r_angle_refined_deg	1.304
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3208
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	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.