2PT7 | pdb_00002pt7

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G6O	PDB ENTRY 1G6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	100mM Mes, 8% polyethylene glycol 8,000, 10mM ethylene-diamine-tetra-acetic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.851	α = 111.04
b = 86.9	β = 95.98
c = 104.129	γ = 104.94

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 210		2006-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97590	ESRF	ID29

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	2.4	94.916	96.3	0.091	0.091	5	3.3	104768	100842	1	1

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	2.4	2.53	96.5		0.243	0.243	2.9	3.5

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	PDB ENTRY 1G6O	2.4	40	104768	95786	5056	96.27	0.23185	0.22986	0.23	0.26966	0.27	RANDOM	33.827

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]
-0.49	-0.01	0.26	0.45	0.1	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.172
r_dihedral_angle_4_deg	17.29
r_dihedral_angle_3_deg	16.584
r_dihedral_angle_1_deg	5.609
r_scangle_it	1.643
r_angle_refined_deg	1.197
r_scbond_it	0.999
r_mcangle_it	0.92
r_mcbond_it	0.589
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.194
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17207
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction