Experiment: 8CEX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	10% w/v PEG4000, 20% v/v glycerol, 0.03M of each ethylene glycol, 0.1M MOPS/HEPES-Na pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.113	α = 90
b = 81.306	β = 90
c = 170.254	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2022-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.3	58.866	100	0.139	0.151	0.057	0.998	9.9	13		50891

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38			2.221	0.543		13.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6G3Y	2.3	58.866	50806	2664	99.921	0.244	0.242	0.2775	68.536

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]
-0.516			0.414		0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.982
r_dihedral_angle_6_deg	16.482
r_dihedral_angle_3_deg	15.447
r_lrange_it	12.658
r_mcangle_it	9.434
r_scangle_it	9.011
r_mcbond_it	6.734
r_scbond_it	6.55
r_dihedral_angle_1_deg	6.433
r_angle_refined_deg	1.407

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.982
r_dihedral_angle_6_deg	16.482
r_dihedral_angle_3_deg	15.447
r_lrange_it	12.658
r_mcangle_it	9.434
r_scangle_it	9.011
r_mcbond_it	6.734
r_scbond_it	6.55
r_dihedral_angle_1_deg	6.433
r_angle_refined_deg	1.407
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.306
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.2
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7375
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
DIALS	data reduction

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 R01GM133198.