7NZH

Crystal structure of HLA-DR4 in complex with a citrullinated cilp peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		290	0.1M sodium acetate trihydrate pH 5.5, 0.2M lithium chloride, 18% (w/v) PEG6000

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.277	α = 90
b = 112.244	β = 90
c = 212.981	γ = 90

Symmetry
Space Group	C 2 2 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 6M-F		2016-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9763	ESRF	ID23-1

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	2.83	56.12	98.6	0.151	0.164	0.061	0.998	14.4	13.3		27807

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	2.83	2.98			1.617	1.749	0.659	0.612		13.2

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	6BIL	2.831	49.698	27756	1402	98.457	0.246	0.2445	0.2833	89.442

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]
-0.283			-1.032		1.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.111
r_dihedral_angle_4_deg	18.103
r_dihedral_angle_3_deg	15.653
r_dihedral_angle_1_deg	9.232
r_lrange_it	9.21
r_lrange_other	9.21
r_scangle_it	4.376
r_scangle_other	4.376
r_mcangle_it	3.389
r_mcangle_other	3.389
r_scbond_it	2.623
r_scbond_other	2.623
r_mcbond_it	2.089
r_mcbond_other	2.085
r_angle_refined_deg	1.622
r_angle_other_deg	1.381
r_symmetry_xyhbond_nbd_other	0.509
r_symmetry_nbd_refined	0.421
r_ext_dist_refined_d	0.312
r_nbd_other	0.228
r_xyhbond_nbd_refined	0.226
r_nbd_refined	0.223
r_symmetry_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.171
r_ncsr_local_group_2	0.096
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_1	0.082
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_bond_other_d	0.011
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6252
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	142

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling