5OX7

Structure of P110 from Mycoplasma genitalium at 2.4A with potassium ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MZB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 3350 21% 0.2M Tri-potassium citrate
Crystal Properties
Matthews coefficientSolvent content
3.6766.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.603α = 90
b = 151.293β = 90
c = 176.245γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray78PIXELDECTRIS PILATUS 2M2016-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97895ALBAXALOC

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
12.462.5499.60.04915.33.456936
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.80.7380.8770.4690.7061.83.48248

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 REPLACEMENTTHROUGHOUT5MZB2.462.5454151277099.430.193630.191290.23971RANDOM74.37
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]
-2.681.621.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.723
r_dihedral_angle_3_deg19.702
r_dihedral_angle_4_deg14.722
r_dihedral_angle_1_deg9.079
r_long_range_B_other8.919
r_long_range_B_refined8.916
r_mcangle_it6.267
r_mcangle_other6.266
r_scangle_other5.989
r_mcbond_it3.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.723
r_dihedral_angle_3_deg19.702
r_dihedral_angle_4_deg14.722
r_dihedral_angle_1_deg9.079
r_long_range_B_other8.919
r_long_range_B_refined8.916
r_mcangle_it6.267
r_mcangle_other6.266
r_scangle_other5.989
r_mcbond_it3.9
r_mcbond_other3.894
r_scbond_it3.843
r_scbond_other3.843
r_angle_refined_deg2.37
r_angle_other_deg1.31
r_chiral_restr0.143
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms6818
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing