1WBD | pdb_00001wbd

Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38Q mutant, in complex with a G.T mismatch


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E3MPDB ENTRY 1E3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525 MM HEPES(7.5), 300 MM NACL, 10 MM MGCL2, 14 % PEG 6000., pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.656.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.62α = 90
b = 92.042β = 90
c = 260.977γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2004-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.42099.30.1211.96.728507343.64
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)
12.42.4992.90.691.785.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E3M2.42082938164499.30.2130.2120.210.2590.26SAME AS FOR ENTRY 1E3M16.95
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]
-2.3354.673-2.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.327
r_scangle_it2.766
r_scbond_it1.651
r_angle_refined_deg1.452
r_mcangle_it0.987
r_angle_other_deg0.856
r_mcbond_it0.513
r_symmetry_vdw_other0.236
r_nbd_other0.225
r_nbd_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.327
r_scangle_it2.766
r_scbond_it1.651
r_angle_refined_deg1.452
r_mcangle_it0.987
r_angle_other_deg0.856
r_mcbond_it0.513
r_symmetry_vdw_other0.236
r_nbd_other0.225
r_nbd_refined0.202
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.108
r_nbtor_other0.087
r_chiral_restr0.076
r_bond_refined_d0.014
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12171
Nucleic Acid Atoms714
Solvent Atoms247
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling