3EXV | pdb_00003exv

Crystal structure of the human Adenovirus type 11 fiber knob

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H7Z	Human Adenovirus type 3 fiber knob

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	18% w/v PEG6000, 0.1M HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.597	α = 90
b = 100.597	β = 90
c = 100.597	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARMOSAIC 225 mm CCD		2006-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1	SLS	X06SA

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	1.45	71	99.9	0.045		6	30079	28526		-3	14.1

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)
	1.45	1.5	100		0.388		5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	Human Adenovirus type 3 fiber knob	1.45	23.71	30079	28526	1525	99.93	0.19365	0.19204	0.2	0.2246	0.23	RANDOM	9.959

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	37.106
r_dihedral_angle_4_deg	12.861
r_dihedral_angle_3_deg	10.705
r_dihedral_angle_1_deg	8.391
r_scangle_it	1.096
r_angle_refined_deg	0.918
r_scbond_it	0.765
r_angle_other_deg	0.679
r_mcangle_it	0.615
r_mcbond_it	0.55
r_symmetry_vdw_other	0.21
r_nbd_other	0.192
r_nbd_refined	0.184
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.108
r_xyhbond_nbd_refined	0.088
r_nbtor_other	0.08
r_symmetry_hbond_refined	0.073
r_chiral_restr	0.059
r_mcbond_other	0.054
r_bond_refined_d	0.005
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	1579
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling