6YXK

Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OCX	5OCX(early model)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20mM Tris pH 7.5, 20mM NaCl, 0.2M ammonium chloride pH 6.3, (20%) w/v PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.379	α = 90
b = 82.094	β = 90
c = 135.613	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 EIGER X 16M		2018-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.91840	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	52.334	99.5	0.122	0.14	0.067	0.996	9.9	8		40933

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.936	1.069	0.511	0.676		8.2

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OCX(early model)	2	52.28	40902	2026	99.513	0.213	0.2105	0.2534	33.325

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]
-0.926			-1.275		2.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.069
r_dihedral_angle_4_deg	21.968
r_dihedral_angle_3_deg	15.786
r_dihedral_angle_1_deg	8.14
r_lrange_it	7.168
r_lrange_other	7.065
r_scangle_it	2.821
r_scangle_other	2.821
r_angle_refined_deg	2.259
r_mcangle_it	2.051
r_mcangle_other	2.051
r_scbond_it	1.842
r_scbond_other	1.838
r_angle_other_deg	1.472
r_mcbond_it	1.344
r_mcbond_other	1.344
r_nbd_other	0.272
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.24
r_symmetry_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.205
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.182
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3395
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Coot	model building
XDS	data scaling