Experiment: 5LKV

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	6.4	277	12 mg/ml DHP B in 20 mM Na cacodylate (pH 6.4) was mixed with a reservoir solution comprising 14-20% (w/v) PEG 4000 and 150-250 mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.359	α = 90
b = 67.359	β = 90
c = 67.522	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		2015-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	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	47.69	95.8	0.022	1	33	3.6		115028			7.6

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	1.08	1.1	71		0.113	0.886	7.6	2.4

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	47.69	109280	5676	95.58	0.1231	0.1222	0.1406	RANDOM	11.182

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]
0.72			-0.26		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.346
r_sphericity_free	25.943
r_dihedral_angle_4_deg	25.52
r_dihedral_angle_3_deg	12.117
r_sphericity_bonded	6.916
r_dihedral_angle_1_deg	4.87
r_rigid_bond_restr	2.518
r_angle_refined_deg	1.633
r_mcangle_it	1.143
r_angle_other_deg	1.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.346
r_sphericity_free	25.943
r_dihedral_angle_4_deg	25.52
r_dihedral_angle_3_deg	12.117
r_sphericity_bonded	6.916
r_dihedral_angle_1_deg	4.87
r_rigid_bond_restr	2.518
r_angle_refined_deg	1.633
r_mcangle_it	1.143
r_angle_other_deg	1.005
r_mcbond_it	0.854
r_mcbond_other	0.854
r_chiral_restr	0.142
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2162
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	128

Software

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