Experiment: 6LER

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UT9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291.15	Calcium chloride, potassium chloride, sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.338	α = 61.5
b = 116.545	β = 82.77
c = 117.9	γ = 64.23

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	98.15	PIXEL	DECTRIS PILATUS 2M-F		2019-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

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	3	48.12	98.6	0.056	0.079	0.056	0.997	12	3.5		88754

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	93.7		0.883	0.883	0.539	1	3.1

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	3ut9	3	48.12	86975	1778	98.6	0.2094	0.2084	0.2609	RANDOM	118.078

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]
1.67	-2.53	0.73	-2.66	1.91	1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.959
r_dihedral_angle_3_deg	18.971
r_dihedral_angle_4_deg	17.584
r_dihedral_angle_1_deg	6.033
r_angle_other_deg	2.321
r_angle_refined_deg	1.152
r_chiral_restr	0.063
r_bond_other_d	0.027
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.959
r_dihedral_angle_3_deg	18.971
r_dihedral_angle_4_deg	17.584
r_dihedral_angle_1_deg	6.033
r_angle_other_deg	2.321
r_angle_refined_deg	1.152
r_chiral_restr	0.063
r_bond_other_d	0.027
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12007
Nucleic Acid Atoms	13862
Solvent Atoms	25
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
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 R01GM133198.