3NWM | pdb_00003nwm

Crystal structure of a single chain construct composed of MHC class I H-2Kd, beta-2microglobulin and a peptide which is an autoantigen for type 1 diabetes

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	20% PEG 8K, TrisHCl pH 8.5, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.347	α = 90
b = 88.527	β = 102.92
c = 61.203	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	CCD	ADSC QUANTUM 315		2009-07-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

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	2.7	50	99.9	0.099	0.077	8.8	4.1		11893

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	99.8		0.536		4.1	594

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2FWO	THROUGHOUT	2.7	59.65	11853	11853	564	99.5	0.2064	0.2064	0.2024	0.2034	0.2844	0.288	RANDOM	43.0386

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]
-1.33		0.93	-3.87		5.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.344
r_dihedral_angle_4_deg	19.903
r_dihedral_angle_3_deg	18.694
r_dihedral_angle_1_deg	6.167
r_mcangle_it	1.597
r_angle_refined_deg	1.159
r_scangle_it	1.138
r_mcbond_it	0.884
r_scbond_it	0.693
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.344
r_dihedral_angle_4_deg	19.903
r_dihedral_angle_3_deg	18.694
r_dihedral_angle_1_deg	6.167
r_mcangle_it	1.597
r_angle_refined_deg	1.159
r_scangle_it	1.138
r_mcbond_it	0.884
r_scbond_it	0.693
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3153
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	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.