Experiment: 6J1C

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	Ammonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.0

Crystal Properties
Matthews coefficient	Solvent content
5.83	78.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.021	α = 90
b = 162.021	β = 90
c = 162.021	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2018-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.09	46.772	99.9	0.071	0.076	0.999	19.44	7.34		41594			37.341

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	2.09	2.22	99.8		0.511	0.551	0.909	3.54	7.271

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	5Y00	2.09	46.77	39511	2080	99.95	0.162	0.1613	0.1769	RANDOM	31.497

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.52
r_dihedral_angle_4_deg	15.411
r_dihedral_angle_3_deg	13.54
r_dihedral_angle_1_deg	7.853
r_angle_refined_deg	2.253
r_angle_other_deg	1.582
r_chiral_restr	0.102
r_bond_refined_d	0.02
r_gen_planes_refined	0.015
r_gen_planes_other	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.52
r_dihedral_angle_4_deg	15.411
r_dihedral_angle_3_deg	13.54
r_dihedral_angle_1_deg	7.853
r_angle_refined_deg	2.253
r_angle_other_deg	1.582
r_chiral_restr	0.102
r_bond_refined_d	0.02
r_gen_planes_refined	0.015
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1811
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	479

Software

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