7O00 | pdb_00007o00

Crystal structure of HLA-DR4 in complex with a HSP70 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J8H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		290	0.03 M of each divalent cation (12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD), 0.1 M MOPS/HEPES-Na pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.23	α = 90
b = 76.23	β = 90
c = 170.66	γ = 90

Symmetry
Space Group	P 43 2 2

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		2016-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.24	56.89	99.8	0.237	0.246	0.066	0.999	12	25.6		25047

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	2.24	2.31			3.474	3.605	0.961	0.635		26.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1J8H	2.24	51.453	22463	1105	89.691	0.201	0.1985	0.2	0.2422	0.25	53.581

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]
-0.036			-0.036		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.629
r_dihedral_angle_3_deg	19.352
r_dihedral_angle_4_deg	17.579
r_dihedral_angle_1_deg	8.263
r_lrange_it	5.844
r_lrange_other	5.826
r_scangle_it	4.008
r_scangle_other	4.007
r_mcangle_it	2.809
r_mcangle_other	2.808
r_scbond_it	2.486
r_scbond_other	2.484
r_mcbond_it	1.764
r_mcbond_other	1.764
r_angle_refined_deg	1.659
r_angle_other_deg	1.213
r_symmetry_xyhbond_nbd_refined	0.228
r_symmetry_nbd_refined	0.201
r_nbd_refined	0.199
r_nbd_other	0.19
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.174
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3057
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	42

Software

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