7OP2 | pdb_00007op2

Chadox1/ Chimpanzee adenovirus Y25 fiber knob protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KNB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M CaCl2, 0.1 M MgCl2, 0.1 M PIPES pH7.0, 22.5 % v/v PEG Smear Medium and 0.2 M CaCl2, 0.1 M Tris pH8.0, 20 % w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.427	α = 90
b = 112.26	β = 92.61
c = 98.605	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	PIXEL	DECTRIS EIGER2 XE 16M		2021-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.59	74.04	100	0.288	0.3	0.084	0.996	5.7	12.7		286462

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	1.59	1.68	99.9		3.342	3.476	0.948	0.367		13.4

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	1KNB	1.59	74.04	271539	14210	99.74	0.2248	0.2238	0.2192	0.2441	0.2379	RANDOM	24.827

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]
0.66			-1.41		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.853
r_dihedral_angle_4_deg	16.69
r_dihedral_angle_3_deg	12.598
r_dihedral_angle_1_deg	7.927
r_angle_refined_deg	1.498
r_angle_other_deg	1.339
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17093
Nucleic Acid Atoms
Solvent Atoms	1206
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data scaling