2RAS

Crystal structure of a putative tetr/acrr family transcriptional regulator (saro_0558) from novosphingobium aromaticivorans dsm at 1.80 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.8277NANODROP, 0.2M MgCl2, 20.0% PEG 3350, No Buffer pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6453.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.5α = 90
b = 76.42β = 90
c = 104.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2007-07-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97925, 0.97901SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.829.70996.70.03414.0147914-327.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8693.90.4322

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.829.70947877241398.770.1780.1770.206RANDOM34.359
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]
2.13-0.23-1.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.8
r_dihedral_angle_4_deg15.251
r_dihedral_angle_3_deg11.949
r_scangle_it6.269
r_scbond_it4.459
r_dihedral_angle_1_deg3.534
r_mcangle_it2.571
r_mcbond_it1.777
r_angle_other_deg1.427
r_angle_refined_deg1.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.8
r_dihedral_angle_4_deg15.251
r_dihedral_angle_3_deg11.949
r_scangle_it6.269
r_scbond_it4.459
r_dihedral_angle_1_deg3.534
r_mcangle_it2.571
r_mcbond_it1.777
r_angle_other_deg1.427
r_angle_refined_deg1.422
r_mcbond_other0.411
r_symmetry_vdw_other0.198
r_nbd_refined0.192
r_nbtor_refined0.162
r_nbd_other0.145
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.121
r_symmetry_vdw_refined0.098
r_chiral_restr0.094
r_nbtor_other0.075
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3133
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing