1LDP | pdb_00001ldp

CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES

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		6.5		PROTEIN WAS CRYSTALLIZED FROM 100MM SODIUM CACODYLATE, 0.2M AMMONIUM SULFATE, 0.5M SODIUM BROMIDE, 30% PEG 8000, PH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
3.18	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.4	α = 90
b = 48.98	β = 97.95
c = 84.06	γ = 90

Symmetry
Space Group	P 1 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	298	AREA DETECTOR	SIEMENS	DOUBLE-MIRROR FOCUSING CAMERAS	1996-01-28	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-18

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	15	81	0.113	0.113	5.6	2.2		11809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.9	63.6		0.358	0.358	1.8	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HOC	3.1	6	1	7935	556	85	0.221	0.221	0.371	RANDOM	28

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]
-4.192		-6.204	2.918		1.274

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	25.8
x_angle_deg	1.8
x_improper_angle_d	1.8
x_bond_d	0.015
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3087
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XDS	data scaling
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

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.