5GKR

Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QHK	4QHK, 4Y5Y, 4IDJ, and 4LLW
experimental model	PDB	4Y5Y	4QHK, 4Y5Y, 4IDJ, and 4LLW
experimental model	PDB	4IDJ	4QHK, 4Y5Y, 4IDJ, and 4LLW
experimental model	PDB	4LLW	4QHK, 4Y5Y, 4IDJ, and 4LLW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Tris-HCl (pH 7.0), 0.2 M NaCl, 1 M Sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.515	α = 90
b = 147.515	β = 90
c = 112.807	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2015-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.1	50	100	0.115	23.1	5.8		53509

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.857	2.6	5.6

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	4QHK, 4Y5Y, 4IDJ, and 4LLW	2.1	26.33	50879	2609	99.98	0.16359	0.16253	0.18512	RANDOM	39.752

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]
-2.08			-2.08		4.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.268
r_dihedral_angle_4_deg	13.916
r_dihedral_angle_3_deg	13.369
r_dihedral_angle_1_deg	6.646
r_long_range_B_refined	2.927
r_long_range_B_other	2.927
r_angle_refined_deg	1.295
r_angle_other_deg	1.051
r_mcangle_it	0.961
r_mcangle_other	0.961
r_scangle_other	0.882
r_mcbond_it	0.545
r_mcbond_other	0.545
r_scbond_it	0.515
r_scbond_other	0.508
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6239
Nucleic Acid Atoms	64
Solvent Atoms	156
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing