Experiment: 6QRI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.5 M lithium chloride, 100 mM Tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), 28 % (w/v) polyethylenglycol 6000, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.54	α = 90
b = 78.619	β = 115.11
c = 77.055	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 2M		2017-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.4	49.2	98.8	0.99	7	3.6		30437

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	95.6		0.47	0.98	3.5

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 (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	1YXQ	2.4	49.16	28923	1523	98.47	0.238	0.2364	0.24	0.2683	0.27	RANDOM	55.698

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]
-1.55		-0.45	0.18		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.55
r_dihedral_angle_4_deg	17.865
r_dihedral_angle_3_deg	14.784
r_dihedral_angle_1_deg	5.468
r_mcangle_it	3.097
r_angle_other_deg	2.308
r_angle_refined_deg	1.947
r_mcbond_it	1.792
r_mcbond_other	1.79
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.55
r_dihedral_angle_4_deg	17.865
r_dihedral_angle_3_deg	14.784
r_dihedral_angle_1_deg	5.468
r_mcangle_it	3.097
r_angle_other_deg	2.308
r_angle_refined_deg	1.947
r_mcbond_it	1.792
r_mcbond_other	1.79
r_chiral_restr	0.116
r_bond_other_d	0.035
r_bond_refined_d	0.014
r_gen_planes_other	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5618
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	188

Software

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