6R41

Structure of P110 from Mycoplasma genitalium complexed with 3'SL


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29319 % PEG3350, 0.2M Tri-potassium citrate
Crystal Properties
Matthews coefficientSolvent content
3.6766.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.026α = 90
b = 151.569β = 90
c = 176.548γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS PILATUS3 6M2016-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.989ALBAXALOC

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
12.2111599.80.99720.64.873757
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)
12.212.330.516

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 REPLACEMENTTHROUGHOUT6R3T2.2111570044370799.70.191060.189750.21568RANDOM71.152
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]
-0.180.33-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.701
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg18.594
r_dihedral_angle_1_deg8.812
r_long_range_B_refined6.332
r_long_range_B_other6.331
r_scangle_other4.209
r_mcangle_it3.581
r_mcangle_other3.581
r_scbond_it2.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.701
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg18.594
r_dihedral_angle_1_deg8.812
r_long_range_B_refined6.332
r_long_range_B_other6.331
r_scangle_other4.209
r_mcangle_it3.581
r_mcangle_other3.581
r_scbond_it2.872
r_scbond_other2.872
r_mcbond_it2.298
r_mcbond_other2.296
r_angle_refined_deg1.809
r_angle_other_deg1.354
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.003
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 Atoms6821
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing