6YXM | pdb_00006yxm

Crystal structure of ACPA 1F2 in complex with CII-C-39-CIT

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20mM Tris pH 7.4, 20mMNaCl, 20% (w/v) PEG 6000, 0.1M HEPES 7.0 pH 7.0, 0.01M zinc chloride.

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.01	α = 90
b = 89.65	β = 90
c = 118.68	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	210	PIXEL	DECTRIS PILATUS3 6M		2018-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97662	Diamond	I03

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	2.85	118.75	99.9	0.146	0.165	0.076	0.993	9.9	8.8		13893

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	2.85	3			0.501	0.569	0.267	0.914		8.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5ocx	2.85	36.219	13539	638	98.137	0.213	0.2098	0.21	0.2762	0.27	39.044

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]
-0.81			0.63		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.407
r_dihedral_angle_4_deg	17.154
r_dihedral_angle_3_deg	16.446
r_dihedral_angle_1_deg	8.123
r_lrange_it	2.348
r_lrange_other	2.345
r_angle_refined_deg	1.333
r_mcangle_it	1.143
r_mcangle_other	1.143
r_angle_other_deg	1.122
r_scangle_it	1.045
r_scangle_other	1.044
r_scbond_it	0.656
r_scbond_other	0.656
r_mcbond_it	0.646
r_mcbond_other	0.645
r_nbd_other	0.273
r_symmetry_nbd_refined	0.267
r_nbd_refined	0.185
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.118
r_xyhbond_nbd_refined	0.117
r_symmetry_metal_ion_refined	0.112
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.044
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3275
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	64

Software

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