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The Crystal Structure of APC from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 (PEG-G2) 0.2M NaAc pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.645 α = 90 b = 46.645 β = 90 c = 114.035 γ = 120
Symmetry Space Group P 32 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 PILATUS3 6M 2021-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
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 2 40.4 99.9 0.065 14 5.6 10243
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 2 2.05 0.74
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 40.396 10243 508 99.718 0.201 0.1979 0.2626 0.2715 43.211
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] -0.921 -0.46 -0.921 2.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.026 r_dihedral_angle_3_deg 12.643 r_lrange_it 9.914 r_lrange_other 9.896 r_scangle_it 8.443 r_scangle_other 8.437 r_scbond_it 5.754 r_scbond_other 5.748 r_mcangle_it 5.036 r_mcangle_other 5.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.026 r_dihedral_angle_3_deg 12.643 r_lrange_it 9.914 r_lrange_other 9.896 r_scangle_it 8.443 r_scangle_other 8.437 r_scbond_it 5.754 r_scbond_other 5.748 r_mcangle_it 5.036 r_mcangle_other 5.035 r_dihedral_angle_2_deg 4.535 r_dihedral_angle_1_deg 3.982 r_mcbond_it 3.941 r_mcbond_other 3.941 r_angle_refined_deg 1.008 r_angle_other_deg 0.368 r_nbd_refined 0.226 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.162 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.106 r_nbd_other 0.103 r_symmetry_nbd_refined 0.089 r_symmetry_nbtor_other 0.066 r_chiral_restr 0.059 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 921 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing