Experiment: 6YLN

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 8000, HEPES, Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.17	α = 90
b = 61.27	β = 90
c = 68.64	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 300K		2019-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

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	1.85	39.27	99.9	0.052	0.053	1	29.51	12.613		18997			38.631

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	1.85	1.9	99.2		1.906	2.058	0.496	0.95	6.809

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	3ztf	1.85	39.27	18046	950	99.88	0.1858	0.184	0.2	0.2179	0.23	RANDOM	42.372

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]
-1.26			1.09		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.922
r_dihedral_angle_3_deg	14.266
r_dihedral_angle_4_deg	8.449
r_dihedral_angle_1_deg	7.436
r_angle_refined_deg	1.711
r_angle_other_deg	0.945
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.922
r_dihedral_angle_3_deg	14.266
r_dihedral_angle_4_deg	8.449
r_dihedral_angle_1_deg	7.436
r_angle_refined_deg	1.711
r_angle_other_deg	0.945
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1776
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	1

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.