1X3E

Crystal structure of the single-stranded DNA-binding protein from Mycobacterium smegmatis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42981M sodium acetate, 500mM sodium chloride, 50mM cadmium sulphate, 20mM Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
237.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.62α = 90
b = 78.62β = 90
c = 79.834γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9BNSLSX9B

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
12.153098.60.0581594615708
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)
12.152.2399.20.492

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1530149131491378798.60.202330.202330.200490.23855RANDOM25.335
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]
-1.67-0.84-1.672.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.52
r_scangle_it3.748
r_scbond_it2.174
r_angle_refined_deg1.393
r_mcangle_it1.277
r_angle_other_deg0.89
r_mcbond_it0.657
r_symmetry_hbond_refined0.489
r_symmetry_vdw_refined0.378
r_symmetry_vdw_other0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.52
r_scangle_it3.748
r_scbond_it2.174
r_angle_refined_deg1.393
r_mcangle_it1.277
r_angle_other_deg0.89
r_mcbond_it0.657
r_symmetry_hbond_refined0.489
r_symmetry_vdw_refined0.378
r_symmetry_vdw_other0.307
r_nbd_other0.258
r_xyhbond_nbd_refined0.218
r_nbd_refined0.211
r_nbtor_other0.083
r_chiral_restr0.08
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1697
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing