1S7W | pdb_00001s7w

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 index peptide and three of its escape variants

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N5A	PDB entry 1N5A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.245	α = 90
b = 123.302	β = 103.13
c = 99.299	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	MARRESEARCH		2003-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.097	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50	99.9			84507	84423		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	99.8

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 1N5A	2.4	19.84	84507	82684	1684	99.99	0.246	0.20008	0.19915	0.21	0.24611	0.26	RANDOM	23.962

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]
-0.03		-0.01	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.416
r_scangle_it	2.963
r_scbond_it	1.776
r_angle_refined_deg	1.491
r_angle_other_deg	1.414
r_mcangle_it	1.292
r_mcbond_it	0.683
r_symmetry_vdw_other	0.275
r_nbd_other	0.243
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.201
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.165
r_chiral_restr	0.092
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12618
Nucleic Acid Atoms
Solvent Atoms	525
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing