6DDV | pdb_00006ddv

Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J8R	4J8R, 1F3D, 1NZ8, 6DDM
experimental model	PDB	1F3D	4J8R, 1F3D, 1NZ8, 6DDM
experimental model	PDB	1NZ8	4J8R, 1F3D, 1NZ8, 6DDM
experimental model	PDB	6DDM	4J8R, 1F3D, 1NZ8, 6DDM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.1 M tri-sodium citrate, 15% isopropanol, 15% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.505	α = 90
b = 89.776	β = 90
c = 89.722	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	35	76	0.09	0.1	0.044	8.9	3.7		26155

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	18.2		0.316	0.421	0.273	0.636		1.2

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	4J8R, 1F3D, 1NZ8, 6DDM	2.05	35	24785	1353	75.94	0.2259	0.2234	0.2283	0.2745	0.2783	RANDOM	38.068

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]
2.05			-0.02		-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.443
r_dihedral_angle_3_deg	13.314
r_dihedral_angle_4_deg	11.608
r_dihedral_angle_1_deg	6.362
r_angle_refined_deg	1.128
r_angle_other_deg	0.836
r_chiral_restr	0.067
r_bond_refined_d	0.006
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	4026
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms

Software

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