Experiment: 6GEB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EWV	2EWV, 5FL3
experimental model	PDB	5FL3	2EWV, 5FL3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	1.2M of Na/K phosphate buffer pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.2	α = 83.7
b = 109.3	β = 86.6
c = 119.8	γ = 60.7

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 PILATUS3 6M		2017-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976250	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.19	36.04	98	6.95	3.49		78104

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	3.19	3.31

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2EWV, 5FL3	3.19	36.04	78095	3841	97.99	0.2345	0.2331	0.23	0.2613	0.26	RANDOM	100.4151

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]
-0.11	0.5	0.36	-0.63	-0.42	1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.303
r_dihedral_angle_4_deg	19.676
r_dihedral_angle_3_deg	19.383
r_dihedral_angle_1_deg	6.911
r_mcangle_it	6.179
r_mcbond_it	3.788
r_mcbond_other	3.788
r_angle_other_deg	3.578
r_angle_refined_deg	1.536
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.303
r_dihedral_angle_4_deg	19.676
r_dihedral_angle_3_deg	19.383
r_dihedral_angle_1_deg	6.911
r_mcangle_it	6.179
r_mcbond_it	3.788
r_mcbond_other	3.788
r_angle_other_deg	3.578
r_angle_refined_deg	1.536
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34602
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
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.