1ZT1

crystal structure of class I MHC H-2Kk in complex with an octapeptide

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	NaCl, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.758	α = 90
b = 111.758	β = 90
c = 109.417	γ = 120

Symmetry
Space Group	P 32 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	CCD	ADSC QUANTUM 4		2003-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9763	ESRF	ID14-4

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	2.5	15	99	0.087	0.069	8.9	2.7	27538	27403	1	1	51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.64	99.2		0.419	0.338	2.1	2.7	3935

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1LEG	2.5	14.87	26053	1344	99.26	0.21202	0.21202	0.21	0.25141	RANDOM	27.161

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]
1.8	0.9		1.8		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.563
r_scangle_it	2.347
r_scbond_it	1.342
r_angle_refined_deg	1.157
r_mcangle_it	0.998
r_angle_other_deg	0.777
r_mcbond_it	0.516
r_symmetry_vdw_other	0.309
r_nbd_other	0.224
r_xyhbond_nbd_refined	0.2
r_nbd_refined	0.178
r_symmetry_hbond_refined	0.12
r_symmetry_vdw_refined	0.087
r_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3132
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	2

Software

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