6QZC | pdb_00006qzc

HLA-DR1 with the QAR Peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	0.1 M Na Cacodylate, 0.2 M NH4 SO4, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.06	α = 90
b = 116.08	β = 90
c = 43.68	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 S 6M		2016-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.64	71.16	99.8	0.094	10.3	7.1		56957

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.68			1.912	0.753	0.518

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	1DLH	1.64	71.156	56904	2819	99.797	0.204	0.2018	0.21	0.2399	0.24	36.371

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]
-1.414			-1.492		2.906

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.518
r_dihedral_angle_1_deg	23.335
r_dihedral_angle_4_deg	17.954
r_dihedral_angle_3_deg	14.971
r_dihedral_angle_other_3_deg	11.96
r_lrange_it	6.927
r_lrange_other	6.866
r_scangle_it	2.263
r_scangle_other	2.257
r_angle_refined_deg	1.687
r_mcangle_it	1.685
r_mcangle_other	1.685
r_scbond_it	1.47
r_scbond_other	1.467
r_angle_other_deg	1.349
r_mcbond_it	1.063
r_mcbond_other	1.063
r_symmetry_nbd_refined	0.271
r_nbd_other	0.212
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.166
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3135
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
XDS	data scaling
PHASER	phasing