☰ Navigation Tabs
PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 74)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PTB 4PTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1M MES pH 6.1 -- 20% PEG20K
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.65 α = 90 b = 45.3 β = 102.42 c = 83.41 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 2M 2015-04-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 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 1.81 42.58 98 0.066 0.078 0.042 0.998 12.8 3.4 41832
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 1.81 1.86 98.7 0.669 0.792 0.42 0.682 3.5 3067
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 4PTB 1.81 42.58 39781 2050 97.64 0.1701 0.1682 0.2067 0.2001 RANDOM 32.941
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] -0.97 0.22 0.21 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.163 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.334 r_mcangle_it 5.379 r_mcbond_it 3.471 r_mcbond_other 3.468 r_angle_refined_deg 1.779 r_angle_other_deg 1.054 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.163 r_dihedral_angle_4_deg 15.034 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.334 r_mcangle_it 5.379 r_mcbond_it 3.471 r_mcbond_other 3.468 r_angle_refined_deg 1.779 r_angle_other_deg 1.054 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2925 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing