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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 1.7 27.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.957 α = 90 b = 26.805 β = 99.662 c = 55.183 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 1.3 54.4 96.7 0.996 9.1 2.9 28411
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 1.3 1.32 87.3 0.417 0.6
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 1.3 54.4 28384 1420 96.132 0.209 0.2074 0.2169 0.2422 0.2528 21.35
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] -0.05 0.18 0.434 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.65 r_dihedral_angle_6_deg 15.3 r_dihedral_angle_2_deg 12.831 r_scangle_it 7.729 r_scangle_other 7.724 r_lrange_it 7.272 r_lrange_other 6.956 r_rigid_bond_restr 6.886 r_scbond_it 6.162 r_scbond_other 6.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.65 r_dihedral_angle_6_deg 15.3 r_dihedral_angle_2_deg 12.831 r_scangle_it 7.729 r_scangle_other 7.724 r_lrange_it 7.272 r_lrange_other 6.956 r_rigid_bond_restr 6.886 r_scbond_it 6.162 r_scbond_other 6.157 r_dihedral_angle_1_deg 5.717 r_mcangle_other 4.244 r_mcangle_it 4.236 r_mcbond_it 3.552 r_mcbond_other 3.549 r_angle_refined_deg 1.445 r_angle_other_deg 0.565 r_nbd_refined 0.242 r_symmetry_nbd_refined 0.215 r_nbd_other 0.211 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.177 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing