3KWW | pdb_00003kww

Crystal structure of the 'restriction triad' mutant of HLA B*3508, beta-2-microglobulin and EBV peptide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.6	298	0.1M cacodlyate, 0.2M ammonium acetate, 18% PEG3350, pH 7.6, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.972	α = 90
b = 81.454	β = 90
c = 110.38	γ = 90

Symmetry
Space Group	P 21 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	298				2008-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1		Australian Synchrotron	MX1

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	2.18	50	99.4	0.057	16.7	3.3	24588	24588

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.18	2.26	99.9		3.8		2428

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 (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	1zhl	2.18	33.67	24588	23559	989	99.46	0.188	0.186	0.18	0.251	0.24	RANDOM	17.066

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]
-0.62			-0.85		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.122
r_dihedral_angle_4_deg	15.875
r_dihedral_angle_3_deg	13.39
r_dihedral_angle_1_deg	5.563
r_scangle_it	3.443
r_scbond_it	2.548
r_mcangle_it	1.532
r_angle_refined_deg	1.04
r_mcbond_it	0.954
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.122
r_dihedral_angle_4_deg	15.875
r_dihedral_angle_3_deg	13.39
r_dihedral_angle_1_deg	5.563
r_scangle_it	3.443
r_scbond_it	2.548
r_mcangle_it	1.532
r_angle_refined_deg	1.04
r_mcbond_it	0.954
r_nbtor_refined	0.295
r_nbd_refined	0.178
r_symmetry_vdw_refined	0.153
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3177
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	90

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.