Experiment: 5K1L

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	15 % PEG 4000 150 mM Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.79	α = 90
b = 68.3	β = 90
c = 68.53	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 2M		2016-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.08	45.41	99.8	0.049	0.999	16.7	6.9		122447

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.08	1.11	99.8		1.44	1.2	5.5

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	3IXF	1.08	45.41	116192	6171	99.8	0.1521	0.1507	0.1772	RANDOM	17.915

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]
0.52			-0.88		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_sphericity_free	28.612
r_dihedral_angle_4_deg	25.307
r_dihedral_angle_3_deg	12.64
r_sphericity_bonded	11.425
r_rigid_bond_restr	6.305
r_dihedral_angle_1_deg	5.445
r_mcangle_it	2.868
r_mcbond_it	2.459
r_mcbond_other	2.459

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_sphericity_free	28.612
r_dihedral_angle_4_deg	25.307
r_dihedral_angle_3_deg	12.64
r_sphericity_bonded	11.425
r_rigid_bond_restr	6.305
r_dihedral_angle_1_deg	5.445
r_mcangle_it	2.868
r_mcbond_it	2.459
r_mcbond_other	2.459
r_angle_other_deg	2.064
r_angle_refined_deg	1.751
r_chiral_restr	0.145
r_bond_refined_d	0.019
r_gen_planes_other	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	119

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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.