Experiment: 7MCM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JCS	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2
experimental model	PDB	4KD6	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2
experimental model	PDB	6L3O	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2
experimental model	PDB	3QMJ	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2
experimental model	PDB	4MI2	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	287	Rigaku Reagents JCSG+ screen, condition B8: 200mM magnesium chloride, 100mM Tris / HCl pH 7.0, 10% (w/v) PEG 8000: MysmA.00358.n.a1.PS00566 at 8.7mg/ml: tray 319818 B8: cryo: 20% EG: puck ACC1-3

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.13	α = 90
b = 104.13	β = 90
c = 83.75	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300	Beryllium Lenses	2021-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.05	50	100	0.063	0.067	0.999	21.54	8.819		32467			40.877

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	2.05	2.1	100		0.633	0.672	0.933	4.03	8.839

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2	2.05	39.7	1.37	32442	1904	99.96	0.1681	0.1661	0.17	0.199	0.2	0	41.15

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
f_dihedral_angle_d	12.1375
f_angle_d	0.8733
f_chiral_restr	0.0582
f_bond_d	0.007
f_plane_restr	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3129
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
MR-Rosetta	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.