4JF8 | pdb_00004jf8

Crystal structure of a TrwG component of type IV secretion system protein from Bartonella birtlesii

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BHM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID 240866a3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.15	α = 90
b = 72.15	β = 90
c = 47.44	γ = 120

Symmetry
Space Group	P 31 2 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 315r		2012-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12709	SSRL	BL7-1

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	1.35	50	99.7	0.038	34.59	8.3	31634	31529		-3

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	1.35	1.39	98.6		0.497	2.9

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	2bhm	1.35	50	29908	1588	99.64	0.15528	0.15426	0.16	0.17514	0.18	RANDOM	15.437

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]
-0.39	-0.2		-0.39		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.202
r_sphericity_free	26.635
r_dihedral_angle_4_deg	20.681
r_dihedral_angle_3_deg	10.988
r_sphericity_bonded	6.73
r_dihedral_angle_1_deg	5.754
r_rigid_bond_restr	1.769
r_mcangle_it	1.353
r_angle_refined_deg	1.304
r_scbond_it	1.207
r_mcbond_it	0.814
r_mcbond_other	0.801
r_angle_other_deg	0.727
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1134
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	16

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction