Experiment: 5QTO

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	33% PEG4000, 0.2 magnesium chloride, 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.26	α = 79.47
b = 59.871	β = 81.46
c = 79.887	γ = 75.59

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 PILATUS 6M		2019-04-22		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.67	41.48	94.2	0.033	0.047	0.033	0.999	9.5	1.7		95026

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	1.67	1.76	93.9		0.885	1.251	0.885	0.432		1.5	13864

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 6GRU	1.67	41.52	89541	4724	93.41	0.231	0.2294	0.24	0.2618	0.28	RANDOM	38.281

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]
2.83	1.15	0.16	-0.65	0.58	-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.375
r_dihedral_angle_3_deg	15.977
r_dihedral_angle_4_deg	13.147
r_dihedral_angle_1_deg	7.547
r_mcangle_it	4.103
r_mcbond_other	2.654
r_mcbond_it	2.64
r_angle_refined_deg	1.518
r_angle_other_deg	1.297
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.375
r_dihedral_angle_3_deg	15.977
r_dihedral_angle_4_deg	13.147
r_dihedral_angle_1_deg	7.547
r_mcangle_it	4.103
r_mcbond_other	2.654
r_mcbond_it	2.64
r_angle_refined_deg	1.518
r_angle_other_deg	1.297
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5784
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	93

Software

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