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Structure of P110 from Mycoplasma genitalium at 2.4A with potassium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350 21%
0.2M Tri-potassium citrate
Crystal Properties Matthews coefficient Solvent content 3.67 66.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.603 α = 90 b = 151.293 β = 90 c = 176.245 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 78 PIXEL DECTRIS PILATUS 2M 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97895 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 62.54 99.6 0.049 15.3 3.4 56936
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) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.8 0.738 0.877 0.469 0.706 1.8 3.4 8248
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 5MZB 2.4 62.54 54151 2770 99.43 0.19363 0.19129 0.196 0.23971 0.2443 RANDOM 74.37
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] -2.68 1.62 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.723 r_dihedral_angle_3_deg 19.702 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_1_deg 9.079 r_long_range_B_other 8.919 r_long_range_B_refined 8.916 r_mcangle_it 6.267 r_mcangle_other 6.266 r_scangle_other 5.989 r_mcbond_it 3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.723 r_dihedral_angle_3_deg 19.702 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_1_deg 9.079 r_long_range_B_other 8.919 r_long_range_B_refined 8.916 r_mcangle_it 6.267 r_mcangle_other 6.266 r_scangle_other 5.989 r_mcbond_it 3.9 r_mcbond_other 3.894 r_scbond_it 3.843 r_scbond_other 3.843 r_angle_refined_deg 2.37 r_angle_other_deg 1.31 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 6818 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing