☰ Navigation Tabs
2.12 A resolution structure of PtxB from Prochlorococcus marinus (MIT 9301) in complex with phosphite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 283 0.1 M Magnesium chloride, 0.1 M sodium citrate pH 5.0 and 15 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.175 α = 90 b = 152.175 β = 90 c = 67.915 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.12 131.79 100 0.086 0.996 7.7 19.1 51504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.16 100 0.733 0.648 1.4 15.7
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 5JVB 2.12 131.79 48734 2541 99.6 0.21993 0.21765 0.2272 0.26396 0.2714 RANDOM 30.215
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] 0.25 0.13 0.25 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.866 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_4_deg 9.122 r_dihedral_angle_1_deg 5.892 r_long_range_B_refined 4.433 r_long_range_B_other 4.42 r_scangle_other 3.323 r_mcangle_it 2.393 r_mcangle_other 2.393 r_scbond_it 2.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.866 r_dihedral_angle_3_deg 13.094 r_dihedral_angle_4_deg 9.122 r_dihedral_angle_1_deg 5.892 r_long_range_B_refined 4.433 r_long_range_B_other 4.42 r_scangle_other 3.323 r_mcangle_it 2.393 r_mcangle_other 2.393 r_scbond_it 2.029 r_scbond_other 2.028 r_mcbond_it 1.518 r_mcbond_other 1.516 r_angle_refined_deg 1.465 r_angle_other_deg 0.945 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6006 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing