7NZE

Crystal structure of HLA-DR4 in complex with a human collagen type II peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		290	20% polyethylene glycol 3350 and 200 mM ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.418	α = 90
b = 71.84	β = 111.331
c = 125.721	γ = 90

Symmetry
Space Group	C 1 2 1

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		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	47.009	98.1	0.999	8.2	1		62583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.1			0.851		1

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	2.05	47.009	62583	3061	97.882	0.194	0.192	0.2449	46.285

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]
-0.63		-0.378	0.592		0.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.774
r_dihedral_angle_4_deg	20.232
r_dihedral_angle_3_deg	16.161
r_dihedral_angle_1_deg	8.377
r_lrange_it	5.653
r_lrange_other	5.58
r_scangle_it	3.063
r_scangle_other	3.062
r_mcangle_it	2.396
r_mcangle_other	2.396
r_scbond_it	1.911
r_scbond_other	1.911
r_angle_refined_deg	1.844
r_mcbond_it	1.528
r_mcbond_other	1.528
r_angle_other_deg	1.318
r_symmetry_nbd_refined	0.415
r_nbd_other	0.268
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6330
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	data reduction
REFMAC	refinement
xia2	data reduction
Aimless	data scaling