Experiment: 5LK9

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	277	12 mg/ml protein in 20 mM cacodylate pH 6.4 Reservoir 18% PEG 4000, 200 mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.25	α = 90
b = 68.41	β = 90
c = 68.43	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		2016-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9163	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	1.12	48.4	98.3	0.035	0.999	50.4	6.1		108968

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.15	98.4		0.926	0.576	1.3	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.12	48.38	103485	5388	98.18	0.1441	0.1429	0.1665	RANDOM	13.963

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]
0.82			-0.21		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.945
r_dihedral_angle_4_deg	24.308
r_sphericity_free	21.544
r_dihedral_angle_3_deg	11.76
r_rigid_bond_restr	7.092
r_sphericity_bonded	6.735
r_dihedral_angle_1_deg	4.848
r_angle_refined_deg	1.764
r_mcangle_it	1.597
r_angle_other_deg	1.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.945
r_dihedral_angle_4_deg	24.308
r_sphericity_free	21.544
r_dihedral_angle_3_deg	11.76
r_rigid_bond_restr	7.092
r_sphericity_bonded	6.735
r_dihedral_angle_1_deg	4.848
r_angle_refined_deg	1.764
r_mcangle_it	1.597
r_angle_other_deg	1.523
r_mcbond_other	1.197
r_mcbond_it	1.196
r_chiral_restr	0.179
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.012
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	136

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.