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The Crystal Structure of Apaf from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6M Na/KPO4 pH6.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.641 α = 90 b = 75.336 β = 90 c = 161.067 γ = 90
Symmetry Space Group P 2 21 21
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 EIGER X 9M 2020-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.1806 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 48.75 100 0.036 29.9 9.5 18178
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.843
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.85 37.696 9582 470 99.584 0.228 0.225 0.2311 0.2831 0.2893 41.291
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] -2.255 5.109 -2.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.684 r_dihedral_angle_2_deg 15.465 r_dihedral_angle_6_deg 14.349 r_dihedral_angle_1_deg 5.336 r_angle_refined_deg 0.965 r_angle_other_deg 0.327 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.684 r_dihedral_angle_2_deg 15.465 r_dihedral_angle_6_deg 14.349 r_dihedral_angle_1_deg 5.336 r_angle_refined_deg 0.965 r_angle_other_deg 0.327 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_nbd_other 0.181 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.134 r_ncsr_local_group_5 0.13 r_ncsr_local_group_6 0.121 r_ncsr_local_group_2 0.118 r_ncsr_local_group_1 0.115 r_ncsr_local_group_3 0.113 r_ncsr_local_group_4 0.097 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3042 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing