8RAL | pdb_00008ral

CL3E peptide bound to the I-Ab murine MHC class II receptor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.2 M magnesium chloride hexahydrate, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.057	α = 90
b = 76.032	β = 90
c = 133.037	γ = 90

Symmetry
Space Group	P 2 21 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		2022-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979181	ALBA	XALOC

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	2.1	46.85	99.2	0.087	0.112	0.07	0.997	7.5	4.3		30076			40.37

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	2.1	2.16			0.936	1.199	0.739	0.783	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1	46.85	30056	1495	98.732	0.219	0.2165	0.2235	0.263	0.2678	45.744

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]
6.844			-6.063		-0.781

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_6_deg	12.761
r_lrange_it	8.475
r_lrange_other	8.475
r_dihedral_angle_1_deg	7.97
r_scangle_it	7.083
r_scangle_other	7.082
r_dihedral_angle_2_deg	6.054
r_mcangle_it	5.897
r_mcangle_other	5.896
r_scbond_it	5.195
r_scbond_other	5.193
r_mcbond_it	4.307
r_mcbond_other	4.304
r_angle_refined_deg	1.688
r_angle_other_deg	0.588
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.209
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.187
r_nbd_other	0.175
r_symmetry_nbd_refined	0.172
r_symmetry_nbtor_other	0.117
r_symmetry_xyhbond_nbd_other	0.111
r_symmetry_xyhbond_nbd_refined	0.11
r_chiral_restr	0.08
r_bond_refined_d	0.007
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	2816
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	69

Software

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