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Structure of P110 from Mycoplasma genitalium complexed with 3'SL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 19 % PEG3350, 0.2M Tri-potassium citrate
Crystal Properties Matthews coefficient Solvent content 3.67 66.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.026 α = 90 b = 151.569 β = 90 c = 176.548 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS3 6M 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.989 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.21 115 99.8 0.997 20.6 4.8 73757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.33 0.516
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6R3T 2.21 115 70044 3707 99.7 0.19106 0.18975 0.1935 0.21568 0.2177 RANDOM 71.152
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] -0.18 0.33 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.351 r_dihedral_angle_3_deg 18.594 r_dihedral_angle_1_deg 8.812 r_long_range_B_refined 6.332 r_long_range_B_other 6.331 r_scangle_other 4.209 r_mcangle_it 3.581 r_mcangle_other 3.581 r_scbond_it 2.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.351 r_dihedral_angle_3_deg 18.594 r_dihedral_angle_1_deg 8.812 r_long_range_B_refined 6.332 r_long_range_B_other 6.331 r_scangle_other 4.209 r_mcangle_it 3.581 r_mcangle_other 3.581 r_scbond_it 2.872 r_scbond_other 2.872 r_mcbond_it 2.298 r_mcbond_other 2.296 r_angle_refined_deg 1.809 r_angle_other_deg 1.354 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 6821 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing