2OBP

Crystal structure of a putative dna-binding protein (reut_b4095) from ralstonia eutropha jmp134 at 1.70 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP5.82770.2M MgNO3, 20.0% PEG-3350, No Buffer pH 5.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8957.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.58α = 90
b = 76.58β = 90
c = 137.86γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2006-12-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97932, 0.97910SSRLBL11-1

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
11.729.41298.20.06319.022699630.103
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)
11.71.7690.90.6283.14479

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 DIFFRACTIONMADTHROUGHOUT1.729.41226956135199.710.1880.1860.219RANDOM20.67
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]
1.060.531.06-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg19.184
r_dihedral_angle_3_deg12.018
r_scangle_it5.665
r_dihedral_angle_1_deg5.55
r_scbond_it4.335
r_mcangle_it2.397
r_mcbond_it1.927
r_angle_refined_deg1.511
r_angle_other_deg1.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.266
r_dihedral_angle_4_deg19.184
r_dihedral_angle_3_deg12.018
r_scangle_it5.665
r_dihedral_angle_1_deg5.55
r_scbond_it4.335
r_mcangle_it2.397
r_mcbond_it1.927
r_angle_refined_deg1.511
r_angle_other_deg1.009
r_mcbond_other0.636
r_xyhbond_nbd_other0.225
r_nbd_refined0.221
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.208
r_symmetry_vdw_refined0.202
r_symmetry_vdw_other0.198
r_nbd_other0.195
r_nbtor_refined0.173
r_chiral_restr0.097
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1177
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms5

Software

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