1X3F

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 acetate, 20mM Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.728.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.014α = 90
b = 78.014β = 90
c = 71.018γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.72099.40.01172197150
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)
12.72.81000.526

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 REPLACEMENTTHROUGHOUT2.7206392639269899.550.207520.207520.200420.27459RANDOM45.56
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]
-2.58-1.29-2.583.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.65
r_scangle_it5.705
r_scbond_it2.974
r_mcangle_it2.911
r_angle_refined_deg1.576
r_mcbond_it1.546
r_angle_other_deg0.863
r_symmetry_hbond_refined0.502
r_symmetry_vdw_refined0.285
r_symmetry_vdw_other0.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.65
r_scangle_it5.705
r_scbond_it2.974
r_mcangle_it2.911
r_angle_refined_deg1.576
r_mcbond_it1.546
r_angle_other_deg0.863
r_symmetry_hbond_refined0.502
r_symmetry_vdw_refined0.285
r_symmetry_vdw_other0.265
r_xyhbond_nbd_refined0.249
r_nbd_other0.242
r_nbd_refined0.229
r_nbtor_other0.09
r_chiral_restr0.087
r_metal_ion_refined0.031
r_bond_refined_d0.017
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
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_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 Atoms1629
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing