☰ Navigation Tabs
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102951
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T3P 5T3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Crystal Properties Matthews coefficient Solvent content 4.09 69.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.8 α = 90 b = 123.8 β = 90 c = 41.06 γ = 120
Symmetry Space Group P 3 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 2017-09-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.57 53.61 99.3 0.122 0.129 0.043 0.997 8.2 7.7 50185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.61 97.5 2.865 3.147 1.28 0.534 5.8 3598
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 FOURIER SYNTHESIS THROUGHOUT 5T3P 1.57 107.21 47257 2425 98.2 0.196 0.194 0.233 0.229 RANDOM 30.8
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] -1.63 -0.82 -1.63 5.3
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.604 r_dihedral_angle_2_deg 29.918 r_sphericity_bonded 22.817 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.297 r_mcangle_it 5.753 r_mcbond_it 4.727 r_mcbond_other 4.724 r_rigid_bond_restr 2.779
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.604 r_dihedral_angle_2_deg 29.918 r_sphericity_bonded 22.817 r_dihedral_angle_4_deg 16.049 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.297 r_mcangle_it 5.753 r_mcbond_it 4.727 r_mcbond_other 4.724 r_rigid_bond_restr 2.779 r_angle_refined_deg 1.813 r_angle_other_deg 1.057 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2) r_scbond_it SIDE-CHAIN BOND OTHER ATOMS (A**2) r_scangle_it SIDE-CHAIN ANGLE OTHER ATOMS (A**2) LONG RANGE B REFINED ATOMS (A**2) LONG RANGE B OTHER ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1449 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing