☰ Navigation Tabs
Crystal Structure Analysis of the HPPK-DHPS in complex with substrates
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG3350, 0.2M Potassium citrate tribasic monohydrate
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.049 α = 90 b = 113.892 β = 94.24 c = 172.387 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 PILATUS3 S 6M 2017-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.79 49.82 99.4 0.9 4.5 3.5 129475
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 2.79 2.84 90.41 0.2 0.7
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 1EYE 2.9 49.82 114185 2006 99.7 0.24263 0.24186 0.2484 0.28542 0.2819 RANDOM 43.362
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] -6.79 -1.17 2.35 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.023 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 17.032 r_dihedral_angle_1_deg 6.775 r_angle_refined_deg 1.643 r_angle_other_deg 0.837 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.023 r_dihedral_angle_4_deg 18.189 r_dihedral_angle_3_deg 17.032 r_dihedral_angle_1_deg 6.775 r_angle_refined_deg 1.643 r_angle_other_deg 0.837 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28365 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 342
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction xia2 data reduction DIALS data scaling