Experiment: 7MYL

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	22% PEG3350, 0.1M Na-Cacodylate pH 6.5, 0.36M MgCl2 and 2 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.072	α = 90
b = 72.89	β = 90.56
c = 125.122	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	PIXEL	DECTRIS EIGER X 9M		2020-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

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	2.15	72.89	98.6	0.19	0.206	0.078	0.993	7.6	6.8		53224			23.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	97.8		0.905	0.983	0.379	0.558	1.9	6.6

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	5ECC	2.15	63.06	50486	2718	98.34	0.2173	0.2147	0.2659	RANDOM	29.331

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]
-0.6		-0.63	2.38		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.538
r_dihedral_angle_4_deg	21.277
r_dihedral_angle_3_deg	18.029
r_dihedral_angle_1_deg	9.153
r_angle_refined_deg	1.414
r_angle_other_deg	1.15
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.538
r_dihedral_angle_4_deg	21.277
r_dihedral_angle_3_deg	18.029
r_dihedral_angle_1_deg	9.153
r_angle_refined_deg	1.414
r_angle_other_deg	1.15
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7442
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.