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1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate
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 5 290 0.2 M Magnesium chloride, 0.1 M Sodium acetate pH 5.0 and 20 % (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.481 α = 84.82 b = 53.703 β = 78.26 c = 66.388 γ = 69.74
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 PILATUS 6M 2016-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97629 Diamond I03
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 1.41 65.05 95.2 0.032 0.999 9.1 3.3 91920
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 1.41 1.43 75.4 0.664 0.48 1.1 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5JVB 1.41 64.98 86075 4350 93.66 0.18221 0.1798 0.23031 0.2284 RANDOM 26.361
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] 0.92 0.69 -0.29 0.15 -0.18 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_sphericity_bonded 31.373 r_sphericity_free 20.522 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 12.98 r_scbond_it 9.544 r_scbond_other 9.544 r_rigid_bond_restr 8.723 r_scangle_other 8.096 r_long_range_B_refined 6.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.506 r_sphericity_bonded 31.373 r_sphericity_free 20.522 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 12.98 r_scbond_it 9.544 r_scbond_other 9.544 r_rigid_bond_restr 8.723 r_scangle_other 8.096 r_long_range_B_refined 6.458 r_long_range_B_other 6.458 r_dihedral_angle_1_deg 5.876 r_mcangle_other 4.089 r_mcangle_it 4.088 r_mcbond_it 3.891 r_mcbond_other 3.891 r_angle_refined_deg 1.514 r_angle_other_deg 1.109 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3998 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing