3FOL | pdb_00003fol

Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFERI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	25% PEG 3350, 200 mM ammonium sulfate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.393	α = 90
b = 66.63	β = 93.66
c = 56.211	γ = 90

Symmetry
Space Group	C 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	100	IMAGE PLATE	RIGAKU RAXIS IV++		2007-03-27		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.3	50	97.4	0.068	19.169	7.1		18990

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	2.3	2.38	76.4		0.819		4.2	1477

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.5	19.84	15063	757	99.91	0.196	0.192	0.1967	0.261	0.2485	RANDOM	39.517

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]
0.02		0.02	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.552
r_dihedral_angle_3_deg	21.473
r_dihedral_angle_4_deg	20.106
r_dihedral_angle_1_deg	6.933
r_scbond_it	3.463
r_mcangle_it	2.418
r_angle_refined_deg	1.601
r_mcbond_it	0.985
r_scangle_it	0.839
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.552
r_dihedral_angle_3_deg	21.473
r_dihedral_angle_4_deg	20.106
r_dihedral_angle_1_deg	6.933
r_scbond_it	3.463
r_mcangle_it	2.418
r_angle_refined_deg	1.601
r_mcbond_it	0.985
r_scangle_it	0.839
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3117
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
PHASER	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.