Experiment: 6AYC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	33% PEG MME 550, 0.03 M CaCl2, 3% Jeffamine M-600, 0.1 M bis-Tris propane, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.3	α = 90
b = 55.19	β = 100.62
c = 72.39	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	DECTRIS PILATUS3 S 6M	MIRRORS	2017-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	2.6	71.15	99.7	0.133	0.146	0.995	7.14	6.535		14541		-3	85.962

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	2.6	2.67	99.8		2.865	3.1	0.303	0.59	6.874

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	5TL8	2.6	71.15	13816	724	99.6	0.2217	0.2183	0.22	0.29	0.29	RANDOM	95.087

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]
0.88		-6.13	1.65		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.602
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	16.292
r_dihedral_angle_1_deg	5.937
r_angle_refined_deg	1.938
r_angle_other_deg	0.921
r_chiral_restr	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.602
r_dihedral_angle_4_deg	20.24
r_dihedral_angle_3_deg	16.292
r_dihedral_angle_1_deg	5.937
r_angle_refined_deg	1.938
r_angle_other_deg	0.921
r_chiral_restr	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3577
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	141

Software

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

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.