Experiment: 6G8R

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.2 M sodium malonate, 0.5 % jeffamine ED-2003, 0.1 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.2	α = 90
b = 89.2	β = 90
c = 343.35	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS PILATUS3 6M		2017-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96861	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.74	64.11	99.5	0.225	0.237	0.997	8.93	10.531		22312			69.035

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.81	99.7		3.23	3.394	0.442	0.72	10.594

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	2MD8, 5FBO, 5GS3	2.74	64.11	21107	1140	99.54	0.2169	0.2152	0.2492	RANDOM	77.703

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]
0.55	0.27		0.55		-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.94
r_dihedral_angle_4_deg	15.022
r_dihedral_angle_3_deg	14.893
r_dihedral_angle_1_deg	6.555
r_angle_refined_deg	1.301
r_angle_other_deg	1.128
r_chiral_restr	0.043
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.94
r_dihedral_angle_4_deg	15.022
r_dihedral_angle_3_deg	14.893
r_dihedral_angle_1_deg	6.555
r_angle_refined_deg	1.301
r_angle_other_deg	1.128
r_chiral_restr	0.043
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3040
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

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.