1N5A | pdb_00001n5a

Crystal structure of the Murine class I Major Histocompatibility Complex of H-2DB, B2-Microglobulin, and A 9-Residue immunodominant peptide epitope gp33 derived from LCMV

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Ammonium sulfate, ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.08	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.998	α = 90
b = 122.657	β = 103.34
c = 99.18	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MARRESEARCH		2000-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.0292	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.85	20	92.6	0.096	12	2.9	46560	46560			63.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.9	94.4		0.254	9.8	2.9	2453

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HOC	2.85	19.92	43227	43227	2277	100	0.2526	0.25264	0.25128	0.25	0.27861	0.28	RANDOM	11.109

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]
-0.34		-2.6	1.53		-2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.018
r_dihedral_angle_1_deg	4.38
r_scangle_it	3.298
r_angle_refined_deg	2.282
r_scbond_it	1.912
r_mcangle_it	1.305
r_mcbond_it	0.672
r_symmetry_vdw_refined	0.428
r_symmetry_hbond_refined	0.355
r_nbd_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.018
r_dihedral_angle_1_deg	4.38
r_scangle_it	3.298
r_angle_refined_deg	2.282
r_scbond_it	1.912
r_mcangle_it	1.305
r_mcbond_it	0.672
r_symmetry_vdw_refined	0.428
r_symmetry_hbond_refined	0.355
r_nbd_refined	0.31
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.133
r_bond_refined_d	0.031
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12568
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.