Experiment: 6KSM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6KSI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	2.0M Sodium Formate, 0.1M Sodium Acetate pH4.5

Crystal Properties
Matthews coefficient	Solvent content
6.4	80.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.51	α = 90
b = 132.51	β = 90
c = 248.243	γ = 90

Symmetry
Space Group	P 41 2 2

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 16M		2019-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.23	50	99.7	0.125	0.999	10.6	7.2		205262			45.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.23	2.37			2.573	0.424

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	6KSI	2.23	48.18	107720	5386	99.76	0.2275	0.2259	0.2586	RANDOM	47.0476

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]
1.02			1.02		-2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.107
r_dihedral_angle_4_deg	23.951
r_dihedral_angle_3_deg	20.697
r_dihedral_angle_1_deg	6.749
r_mcangle_it	4.787
r_angle_other_deg	3.928
r_mcbond_it	3.299
r_mcbond_other	3.29
r_angle_refined_deg	2.603
r_chiral_restr	0.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.107
r_dihedral_angle_4_deg	23.951
r_dihedral_angle_3_deg	20.697
r_dihedral_angle_1_deg	6.749
r_mcangle_it	4.787
r_angle_other_deg	3.928
r_mcbond_it	3.299
r_mcbond_other	3.29
r_angle_refined_deg	2.603
r_chiral_restr	0.237
r_bond_refined_d	0.025
r_gen_planes_other	0.023
r_gen_planes_refined	0.014
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6040
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	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 R01GM133198.