3HWU

Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22770.2000M NaCl, 20.0000% PEG-1000, 0.1M Na,K-Phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.8935.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.897α = 90
b = 53.897β = 90
c = 111.1γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-03-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91162,0.97929,0.97918SSRLBL9-2

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
11.326.94891.60.02813.782.7129085-311.177
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)
11.31.35640.2582.4

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 DIFFRACTIONMADTHROUGHOUT1.326.94829085149098.580.1210.1190.14RANDOM15.307
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]
0.20.10.2-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.949
r_dihedral_angle_3_deg12.956
r_dihedral_angle_4_deg11.397
r_sphericity_free9.758
r_dihedral_angle_1_deg6.584
r_scangle_it4.475
r_sphericity_bonded3.917
r_scbond_it3.431
r_mcangle_it2.304
r_rigid_bond_restr1.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.949
r_dihedral_angle_3_deg12.956
r_dihedral_angle_4_deg11.397
r_sphericity_free9.758
r_dihedral_angle_1_deg6.584
r_scangle_it4.475
r_sphericity_bonded3.917
r_scbond_it3.431
r_mcangle_it2.304
r_rigid_bond_restr1.899
r_mcbond_it1.833
r_angle_refined_deg1.644
r_angle_other_deg0.845
r_mcbond_other0.719
r_symmetry_vdw_other0.312
r_symmetry_hbond_refined0.308
r_nbd_other0.207
r_nbd_refined0.205
r_xyhbond_nbd_refined0.197
r_nbtor_refined0.175
r_symmetry_vdw_refined0.135
r_chiral_restr0.103
r_nbtor_other0.089
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1101
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms

Software

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