3BCW

Crystal structure of a duf861 family protein with a rmlc-like cupin fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	277	NANODROP, 0.2M MgAcetate, 20.0% PEG 3350, No Buffer pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.01	α = 90
b = 57	β = 90
c = 101.23	γ = 90

Symmetry
Space Group	P 21 21 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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97939	APS	23-ID-D

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	1.6	27.608	95.7	0.049	10.61	2.84		36782		-3	19.06

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	1.6	1.66	95.5		0.497	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	27.608	36750	1826	98.23	0.169	0.167	0.201	RANDOM	15.19

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]
0.73			0.29		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.445
r_dihedral_angle_4_deg	11.309
r_dihedral_angle_3_deg	9.937
r_scangle_it	5.121
r_dihedral_angle_1_deg	4.672
r_scbond_it	3.708
r_mcangle_it	2.3
r_mcbond_it	1.812
r_angle_refined_deg	1.708
r_angle_other_deg	1.411
r_mcbond_other	0.493
r_symmetry_vdw_other	0.249
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.177
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.166
r_chiral_restr	0.103
r_nbtor_other	0.082
r_symmetry_vdw_refined	0.072
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	43

Software

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