Experiment: 4DEM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N46	PDB ENTRY 3N46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	295	30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.23	α = 90
b = 111.23	β = 90
c = 67.724	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	RAYONIX MX-300		2011-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	50	99.9	0.048	0.048	50.4	14.3	36881	36881

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	1.85	1.88	100		0.391	0.391	8	14	1816

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3N46	1.85	50	34866	34866	1837	99.41	0.17545	0.17545	0.17409	0.20176	RANDOM	26.781

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]
-1.72			-1.72		3.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.486
r_dihedral_angle_4_deg	19.371
r_dihedral_angle_3_deg	13.823
r_scangle_it	5.549
r_dihedral_angle_1_deg	4.945
r_scbond_it	3.495
r_mcangle_it	2.342
r_angle_refined_deg	1.749
r_mcbond_it	1.381
r_angle_other_deg	1.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.486
r_dihedral_angle_4_deg	19.371
r_dihedral_angle_3_deg	13.823
r_scangle_it	5.549
r_dihedral_angle_1_deg	4.945
r_scbond_it	3.495
r_mcangle_it	2.342
r_angle_refined_deg	1.749
r_mcbond_it	1.381
r_angle_other_deg	1.111
r_mcbond_other	0.425
r_chiral_restr	0.129
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2742
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	29

Software

Software
Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.