7NZF | pdb_00007nzf

Crystal structure of HLA-DR4 in complex with a mutated 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	1J8H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		290	0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.441	α = 90
b = 71.441	β = 90
c = 138.049	γ = 120

Symmetry
Space Group	P 32 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		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.91842	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	1.9	46.07	99	0.087	0.095	0.039	0.999	17.5	11.1		32456

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	1.9	1.94			0.834	0.913	0.37	0.853		11.5

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	1.9	36.951	32382	1564	98.44	0.224	0.2214	0.23	0.2667	0.27	35.725

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]
0.14	0.07		0.14		-0.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.878
r_dihedral_angle_3_deg	15.723
r_dihedral_angle_4_deg	15.493
r_dihedral_angle_1_deg	8.225
r_lrange_it	4.558
r_lrange_other	4.503
r_scangle_it	1.843
r_scangle_other	1.843
r_angle_refined_deg	1.631
r_mcangle_it	1.525
r_mcangle_other	1.525
r_angle_other_deg	1.293
r_scbond_it	1.158
r_scbond_other	1.157
r_mcbond_it	0.948
r_mcbond_other	0.947
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.189
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.045
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3022
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	28

Software

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