2QYC | pdb_00002qyc

Crystal structure of a dimeric ferredoxin-like protein (bb1511) from bordetella bronchiseptica rb50 at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	NANODROP, 0.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.82	α = 90
b = 50.82	β = 90
c = 142.17	γ = 120

Symmetry
Space Group	P 32 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-07-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926	SSRL	BL11-1

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	1.9	28.433	99.7	0.087	9.74	7.04		17516			23.22

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	1.9	1.97	99.7		0.618	2.52

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 (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	MAD	THROUGHOUT	1.9	28.433	17466	881	99.76	0.18	0.18	0.177	0.18	0.236	0.24	RANDOM	21.44

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]
1.21	0.6		1.21		-1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.7
r_dihedral_angle_4_deg	18.065
r_dihedral_angle_3_deg	13.841
r_scangle_it	7.891
r_scbond_it	6.312
r_dihedral_angle_1_deg	6.169
r_mcangle_it	3.494
r_mcbond_it	2.772
r_angle_refined_deg	1.678
r_angle_other_deg	0.95
r_mcbond_other	0.705
r_symmetry_vdw_other	0.239
r_nbd_refined	0.216
r_nbtor_refined	0.198
r_symmetry_vdw_refined	0.197
r_nbd_other	0.193
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.143
r_chiral_restr	0.093
r_nbtor_other	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1563
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	13

Software

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