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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 5.6 277.15 20% PEG 8000, 0.04M POTASSIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 1.7 27.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.57 α = 90 b = 26.886 β = 100.304 c = 55.645 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 2020-09-16 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 1.35 54.75 98.3 0.996 7.2 2.8 26051
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 1.35 1.37 0.413 0.5
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 (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 1.35 54.748 26019 1322 98.129 0.202 0.1994 0.209 0.2576 0.2594 21.32
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] 0.099 0.827 0.603 -0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.162 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_2_deg 8.939 r_lrange_it 5.902 r_lrange_other 5.755 r_scangle_it 5.42 r_scangle_other 5.417 r_dihedral_angle_1_deg 5.13 r_scbond_it 4.573 r_scbond_other 4.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.162 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_2_deg 8.939 r_lrange_it 5.902 r_lrange_other 5.755 r_scangle_it 5.42 r_scangle_other 5.417 r_dihedral_angle_1_deg 5.13 r_scbond_it 4.573 r_scbond_other 4.569 r_rigid_bond_restr 4.541 r_mcangle_other 3.938 r_mcangle_it 3.933 r_mcbond_it 3.102 r_mcbond_other 3.101 r_angle_refined_deg 1.494 r_angle_other_deg 0.485 r_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.194 r_symmetry_nbd_refined 0.184 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.152 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_symmetry_xyhbond_nbd_other 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing