2OBE | pdb_00002obe

Crystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Major Coat Protein Hexon

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	0.1 M sodium cacodylate, 0.2 M ammonium phosphate, 45% 2-methyl-2,4-pentanediol (MPD), pH 5.0, vapor diffusion, hanging drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.8	α = 90
b = 433	β = 90
c = 159.3	γ = 90

Symmetry
Space Group	C 2 2 2

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	BRANDEIS - B4		2002-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.100	NSLS	X12C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	99	97.7	0.089	15.7	13.1		177830

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	87.8		0.253	4.3	2.8	15823

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1RUX	2.1	49.27	177795	2025	100	0.169	0.169	0.17	0.21	RANDOM	37.687

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]
2.49			-3.11		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.622
r_dihedral_angle_4_deg	21.698
r_dihedral_angle_3_deg	14.768
r_dihedral_angle_1_deg	7.141
r_scangle_it	2.267
r_mcangle_it	2.135
r_angle_refined_deg	1.828
r_scbond_it	1.677
r_mcbond_it	1.457
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.622
r_dihedral_angle_4_deg	21.698
r_dihedral_angle_3_deg	14.768
r_dihedral_angle_1_deg	7.141
r_scangle_it	2.267
r_mcangle_it	2.135
r_angle_refined_deg	1.828
r_scbond_it	1.677
r_mcbond_it	1.457
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.276
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21511
Nucleic Acid Atoms
Solvent Atoms	1521
Heterogen Atoms	302

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.