1KPV | pdb_00001kpv

High resolution crystal structure of the MHC class I complex H-2Kb/SEV9

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VAB	PDB entry 2vab chains A and B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.287	α = 90
b = 88.342	β = 90
c = 45.322	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARRESEARCH		2000-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	32	99.7	0.056	14.9	3.7		60060		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	99.9		0.591	1.4	3.7	2991

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 (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 2vab chains A and B	1.71	32	54406	2890	95.7	0.18761	0.18671	0.2	0.20431	0.21	RANDOM	21.198

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]
-0.74			1.34		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.04
r_scangle_it	5.076
r_dihedral_angle_1_deg	4.734
r_scbond_it	3.054
r_angle_other_deg	2.559
r_mcangle_it	1.989
r_angle_refined_deg	1.784
r_mcbond_it	1.088
r_nbtor_other	0.411
r_symmetry_hbond_refined	0.229
r_nbd_refined	0.222
r_nbd_other	0.21
r_symmetry_hbond_other	0.19
r_symmetry_vdw_other	0.179
r_xyhbond_nbd_refined	0.169
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.153
r_xyhbond_nbd_other	0.036
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.001
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3112
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing