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1.46 A resolution structure of PhnD1 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 8 290 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) buffer pH 8.0 and 25% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.33 α = 90 b = 57.61 β = 107.15 c = 54.79 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97951 Diamond I24
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 1.46 44.27 97.3 0.021 0.999 15.8 3.5 46137
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 1.46 1.49 78.4 0.67 0.569 1.1 2.5
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 1.46 44.27 44161 2244 96.82 0.14764 0.14597 0.18 0.2056 RANDOM 34.119
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] 0.02 -1.47 1.46 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.938 r_sphericity_bonded 30.611 r_sphericity_free 22.292 r_dihedral_angle_3_deg 14.837 r_dihedral_angle_4_deg 13.947 r_scbond_other 11.529 r_scbond_it 11.519 r_scangle_other 9.923 r_rigid_bond_restr 9.18 r_long_range_B_other 7.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.938 r_sphericity_bonded 30.611 r_sphericity_free 22.292 r_dihedral_angle_3_deg 14.837 r_dihedral_angle_4_deg 13.947 r_scbond_other 11.529 r_scbond_it 11.519 r_scangle_other 9.923 r_rigid_bond_restr 9.18 r_long_range_B_other 7.758 r_long_range_B_refined 7.716 r_dihedral_angle_1_deg 5.937 r_mcbond_it 4.433 r_mcangle_other 4.373 r_mcangle_it 4.229 r_mcbond_other 3.679 r_angle_refined_deg 1.468 r_angle_other_deg 1.338 r_chiral_restr 0.169 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2206 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing BUCCANEER model building