Experiment: 6KSL

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	8.5	293	1.0M Ammonium phosphate dibasic, 0.1M Tris pH8.5

Crystal Properties
Matthews coefficient	Solvent content
5.3	76.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.209	α = 90
b = 164.209	β = 90
c = 233.053	γ = 120

Symmetry
Space Group	P 61 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		2018-10-27	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	2.59	50	99.8	0.083	0.999	16.8	10.6		109044			65

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	2.59	2.75			2.138	0.523

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	6KSI	2.59	48.81	58006	2901	99.8	0.2503	0.2493	0.25	0.2675	0.27	RANDOM	65.5405

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	-0.3		-0.6		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.799
r_dihedral_angle_4_deg	24.951
r_dihedral_angle_3_deg	22.649
r_dihedral_angle_1_deg	6.474
r_mcangle_it	6.2
r_mcbond_it	4.314
r_mcbond_other	4.312
r_angle_other_deg	3.93
r_angle_refined_deg	2.122
r_chiral_restr	0.175

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.799
r_dihedral_angle_4_deg	24.951
r_dihedral_angle_3_deg	22.649
r_dihedral_angle_1_deg	6.474
r_mcangle_it	6.2
r_mcbond_it	4.314
r_mcbond_other	4.312
r_angle_other_deg	3.93
r_angle_refined_deg	2.122
r_chiral_restr	0.175
r_bond_refined_d	0.018
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6046
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	58

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 R01GM157729.