3BEW | pdb_00003bew

10mer Crystal Structure of chicken MHC class I haplotype B21

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BEV	PDB ENTRY 3BEV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	27% PEG 3350, 0.1M HEPES pH 7.0, 0.1M MgCl2, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.393	α = 90
b = 88.711	β = 80.01
c = 100.23	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		2005-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97650	ESRF	BM14

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	2.6	30		0.097	0.097	13.2			39205

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)
	2.6	2.69			0.323	0.323	2.8		1560

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 3BEV	2.6	29.15	30179	1514	97.49	0.237	0.234	0.23	0.295	0.29	RANDOM	28.337

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]
3.59		1.67	-1.88		-2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.044
r_dihedral_angle_3_deg	18.94
r_dihedral_angle_4_deg	14.392
r_scangle_it	6.769
r_dihedral_angle_1_deg	6.424
r_scbond_it	5.332
r_mcangle_it	4.752
r_mcbond_it	3.684
r_mcbond_other	1.461
r_angle_refined_deg	1.336
r_angle_other_deg	0.974
r_nbd_refined	0.213
r_symmetry_vdw_other	0.209
r_nbd_other	0.202
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.166
r_chiral_restr	0.115
r_symmetry_vdw_refined	0.1
r_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6104
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing