3QD7

Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62891.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2VAPOR DIFFUSION, HANGING DROP62891.5M ammonium sulfate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.517α = 90
b = 34.833β = 90
c = 40.698γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2010-01-31MSINGLE WAVELENGTH
22x-ray100CCDMARMOSAIC 225 mm CCD2010-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9790SPring-8BL41XU
2SYNCHROTRONSSRF BEAMLINE BL17U1.5028SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,22.3501000.0610.06424.35.96306630611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.32.3898.20.1690.2428.265.5587

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD, MOLECULAR REPLACEMENTTHROUGHOUT2.347.76630663063230.225160.225160.224150.24358RANDOM29.485
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]
-0.890.070.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.297
r_dihedral_angle_4_deg22.424
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg5.877
r_angle_refined_deg1.367
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.297
r_dihedral_angle_4_deg22.424
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg5.877
r_angle_refined_deg1.367
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1043
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing