3BYQ | pdb_00003byq

Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	277	NANODROP, 20% PEG 8000, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.542	α = 90
b = 133.127	β = 90
c = 92.544	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97912	SSRL	BL11-1

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	1.7	29.854	99.2	0.107	0.107	5.9	5		65104			16.3

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	1.7	1.74	96.6		0.716	0.716	1.1	5	4642

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.7	29.854	65081	3297	99.05	0.139	0.138	0.14	0.169	0.17	RANDOM	16.995

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]
-0.6			1.94		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.367
r_dihedral_angle_3_deg	9.509
r_dihedral_angle_4_deg	8.91
r_scangle_it	5.634
r_dihedral_angle_1_deg	4.411
r_scbond_it	3.967
r_mcangle_it	2.429
r_mcbond_it	1.664
r_angle_refined_deg	1.64
r_angle_other_deg	1.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.367
r_dihedral_angle_3_deg	9.509
r_dihedral_angle_4_deg	8.91
r_scangle_it	5.634
r_dihedral_angle_1_deg	4.411
r_scbond_it	3.967
r_mcangle_it	2.429
r_mcbond_it	1.664
r_angle_refined_deg	1.64
r_angle_other_deg	1.396
r_mcbond_other	0.541
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4361
Nucleic Acid Atoms
Solvent Atoms	566
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

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.