Experiment: 5D4G

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris pH 8.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.783	α = 90
b = 73.783	β = 90
c = 129.879	γ = 120

Symmetry
Space Group	P 64 2 2

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	RAYONIX MX300-HS		2015-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.08	50	99.6	0.082	0.085	0.022	11.7	13.9		13123

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.18	99.1		0.83	0.867	0.239	0.662		12.6	1274

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	5D42	2.08	50	12412	690	99.52	0.1832	0.1805	0.2315	RANDOM	48.278

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]
-0.73	-0.37		-0.73		2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.545
r_dihedral_angle_4_deg	19.11
r_dihedral_angle_3_deg	15.461
r_dihedral_angle_1_deg	6.42
r_mcangle_it	3.768
r_mcbond_it	2.724
r_mcbond_other	2.723
r_angle_refined_deg	2.222
r_angle_other_deg	1.135
r_chiral_restr	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.545
r_dihedral_angle_4_deg	19.11
r_dihedral_angle_3_deg	15.461
r_dihedral_angle_1_deg	6.42
r_mcangle_it	3.768
r_mcbond_it	2.724
r_mcbond_other	2.723
r_angle_refined_deg	2.222
r_angle_other_deg	1.135
r_chiral_restr	0.127
r_bond_refined_d	0.023
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1448
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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.