6KYU | pdb_00006kyu

Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I molecule

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	2% v/v Tacsimate TM pH 7.0 0.1 M HEPES pH 7.5 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.468	α = 90
b = 82.468	β = 90
c = 112.507	γ = 120

Symmetry
Space Group	P 62

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 315r		2019-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97931	SSRF	BL18U1

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	1.26	19.85	86.26	0.086	0.086	12.6	14.6		101015

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)
1	1.26	1.3			0.086	0.086

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.5	19.81	69095	3477	99.831	0.167	0.1662	0.1662	0.1878	0.1876	22.042

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.316
r_dihedral_angle_4_deg	17.305
r_dihedral_angle_3_deg	13.826
r_dihedral_angle_1_deg	6.6
r_lrange_it	6.408
r_lrange_other	6.144
r_scangle_it	5.033
r_scangle_other	5.032
r_scbond_it	3.321
r_scbond_other	3.32
r_mcangle_other	2.541
r_mcangle_it	2.54
r_mcbond_it	1.745
r_angle_refined_deg	1.739
r_mcbond_other	1.739
r_angle_other_deg	1.479
r_symmetry_xyhbond_nbd_refined	0.341
r_xyhbond_nbd_other	0.232
r_xyhbond_nbd_refined	0.215
r_nbd_refined	0.207
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.175
r_nbd_other	0.167
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3095
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing