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PanDDA analysis -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277.5 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 1.71 28.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.789 α = 90 b = 27.009 β = 99.944 c = 55.563 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2020-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9127 Diamond I04-1
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 1.55 40.28 99.2 0.96 6 3 17568
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 1.55 1.58 0.544 0.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AV9 1.55 40.28 17561 1078 99.024 0.239 0.2346 0.2411 0.3161 0.3209 19.628
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] 0.42 0.566 0.672 -1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.978 r_dihedral_angle_6_deg 15.676 r_dihedral_angle_2_deg 10.338 r_lrange_it 9.454 r_lrange_other 7.898 r_scangle_it 5.701 r_scangle_other 5.698 r_dihedral_angle_1_deg 5.334 r_scbond_it 4.825 r_scbond_other 4.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.978 r_dihedral_angle_6_deg 15.676 r_dihedral_angle_2_deg 10.338 r_lrange_it 9.454 r_lrange_other 7.898 r_scangle_it 5.701 r_scangle_other 5.698 r_dihedral_angle_1_deg 5.334 r_scbond_it 4.825 r_scbond_other 4.821 r_mcangle_it 4.508 r_mcangle_other 4.506 r_rigid_bond_restr 4.371 r_mcbond_it 3.801 r_mcbond_other 3.797 r_angle_refined_deg 1.389 r_angle_other_deg 0.514 r_nbd_other 0.301 r_nbd_refined 0.249 r_symmetry_nbd_refined 0.249 r_symmetry_nbd_other 0.206 r_symmetry_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.063 r_bond_other_d 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing