3D9X | pdb_00003d9x

Structure of the head of the Bartonella adhesin BadA

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S7M	PDB ENTRY 1s7m

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.05M ammonium sulfate, 0.05M Bis-Tris (pH 6.5), 30% v/v pentaerythrol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.538955	20.075651

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.87	α = 65.87
b = 51.14	β = 76.6
c = 58.62	γ = 82.08

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 315			M	SINGLE WAVELENGTH

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

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	1.13	30	90.7	0.085	3.7	5.8		105179		3.7	13.6

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)
	1.13	1.16	76		0.52	3.7	5.4	14273

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 (All)	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 1s7m	1.13	25	105179	99858	5256	100	0.157	0.15704	0.15592	0.16	0.17801	0.18	RANDOM	10.076

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]
0.1	0.22	-0.15	-0.09	0.23	-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.2
r_dihedral_angle_4_deg	27.203
r_dihedral_angle_3_deg	11.182
r_dihedral_angle_1_deg	6.177
r_sphericity_free	4.429
r_scangle_it	3.419
r_scbond_it	2.623
r_sphericity_bonded	2.521
r_mcangle_it	2.005
r_mcbond_it	1.769
r_angle_refined_deg	1.369
r_rigid_bond_restr	1.345
r_angle_other_deg	0.829
r_mcbond_other	0.471
r_symmetry_vdw_refined	0.226
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.211
r_nbd_other	0.191
r_symmetry_vdw_other	0.188
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2584
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing