6R43

Structure of P110 from Mycoplasma Genitalium complexed with 6'-SL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6R3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29321% PEG 3350, 0.2M Tri-potassium citrate
Crystal Properties
Matthews coefficientSolvent content
3.6866.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.69α = 90
b = 152.69β = 90
c = 176.23γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 315r2016-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97895ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.557.798.40.99918.94.350406
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.560.76

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6R3T2.5257.746747247497.940.190820.189080.22352RANDOM93.318
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]
-0.37-0.881.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.549
r_dihedral_angle_3_deg20.313
r_dihedral_angle_4_deg19.24
r_dihedral_angle_1_deg9.183
r_long_range_B_refined6.639
r_long_range_B_other6.63
r_mcangle_it4.514
r_mcangle_other4.514
r_scangle_other4.443
r_scbond_it2.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.549
r_dihedral_angle_3_deg20.313
r_dihedral_angle_4_deg19.24
r_dihedral_angle_1_deg9.183
r_long_range_B_refined6.639
r_long_range_B_other6.63
r_mcangle_it4.514
r_mcangle_other4.514
r_scangle_other4.443
r_scbond_it2.95
r_scbond_other2.898
r_mcbond_it2.886
r_mcbond_other2.885
r_angle_refined_deg1.901
r_angle_other_deg1.315
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6825
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing