3PWJ | pdb_00003pwj

Human Class I MHC HLA-A2 in complex with the HuD (G2L,I9V) peptide variant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.18	α = 81.98
b = 62.853	β = 76.2
c = 74.698	γ = 78.11

Symmetry
Space Group	P 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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9793	APS	19-BM

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	1.7	20	96.2	0.042	18	1.9	95066	91454	1	1	21.5

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)
	1.7	1.76	92		0.349		1.8	8713

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 1DUZ	1.7	20	95252	91395	4560	95.95	0.1814	0.1814	0.1797	0.206	0.2152	0.2387	RANDOM	26.471

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]
0.72	0.27	0.97	-0.61	0.16	-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.426
r_dihedral_angle_4_deg	21.079
r_dihedral_angle_3_deg	14.918
r_dihedral_angle_1_deg	6.348
r_scangle_it	2.951
r_mcangle_it	2.366
r_scbond_it	1.979
r_angle_refined_deg	1.773
r_mcbond_it	1.474
r_chiral_restr	0.142
r_bond_refined_d	0.017
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6324
Nucleic Acid Atoms
Solvent Atoms	693
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction