Experiment: 6YZP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	291	1.6 M sodium citrate, 50 mM Tris-H2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.814	α = 90
b = 41.074	β = 103.86
c = 72.24	γ = 90

Symmetry
Space Group	P 1 21 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		2018-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.35	40.6	97.5	0.076	0.088	0.998	9.25	3.773		51336			21.52

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	1.35	1.43	96.3		1.134	1.319	0.528	1.07	3.789

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	FOURIER SYNTHESIS	THROUGHOUT	6GXE	1.35	40.6	48771	2567	97.57	0.1779	0.1768	0.1982	RANDOM	19.567

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]
-1.22		-0.25	-0.27		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.738
r_dihedral_angle_4_deg	17.548
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	7.29
r_angle_refined_deg	1.653
r_angle_other_deg	1.522
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_bond_other_d	0.01
r_gen_planes_refined	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.738
r_dihedral_angle_4_deg	17.548
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	7.29
r_angle_refined_deg	1.653
r_angle_other_deg	1.522
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_bond_other_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2044
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	22

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
FFT	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 R01GM133198.