Experiment: 7MKC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XFX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	PEG 3350, NaI, Sodium Cacodylate, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.358	α = 90
b = 90.358	β = 90
c = 55.695	γ = 120

Symmetry
Space Group	P 6

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 PILATUS3 6M		2020-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03317	APS	23-ID-D

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	2.65	45.38	98.5	0.092	0.101	0.041	0.998	11.2	5.5		7562

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	2.65	2.78	96.8		0.774	0.858	0.359	0.643		5.3

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	4XFX	2.65	45.38	7190	366	98.63	0.1858	0.1828	0.2421	RANDOM	66.778

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]
-0.31	-0.15		-0.31		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	63.808
r_sphericity_free	55.905
r_dihedral_angle_2_deg	37.574
r_dihedral_angle_3_deg	17.27
r_dihedral_angle_4_deg	17.093
r_dihedral_angle_1_deg	6.488
r_angle_refined_deg	1.96
r_angle_other_deg	1.138
r_chiral_restr	0.113
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	63.808
r_sphericity_free	55.905
r_dihedral_angle_2_deg	37.574
r_dihedral_angle_3_deg	17.27
r_dihedral_angle_4_deg	17.093
r_dihedral_angle_1_deg	6.488
r_angle_refined_deg	1.96
r_angle_other_deg	1.138
r_chiral_restr	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1725
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	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.