Experiment: 6IRI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100 mM HEPES (pH 7.5), 2.4 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.72	28.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.946	α = 90
b = 51.121	β = 116.15
c = 31.57	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	CCD	ADSC QUANTUM 315		2018-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.38	28.34	99.3	0.056	0.999	12.82	3.68		16325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.47	98.9		0.585	0.718	2	3.62

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	MOLECULAR REPLACEMENT	THROUGHOUT	5AUI	1.38	28.34	15531	793	99.7	0.1146	0.1124	0.157	RANDOM	18.168

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]
-0.03		-0.32	1.18		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.356
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	12.446
r_sphericity_bonded	10.86
r_dihedral_angle_4_deg	10.182
r_rigid_bond_restr	9.159
r_dihedral_angle_1_deg	6.448
r_angle_refined_deg	2.086
r_angle_other_deg	1.154
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.356
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	12.446
r_sphericity_bonded	10.86
r_dihedral_angle_4_deg	10.182
r_rigid_bond_restr	9.159
r_dihedral_angle_1_deg	6.448
r_angle_refined_deg	2.086
r_angle_other_deg	1.154
r_chiral_restr	0.132
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	821
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	9

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.