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Crystal structure of Apo PSD from E. coli (2.63 A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.18 M Ammonium acetate, 0.09 M Tris pH 8.5, 22.5% w/v PEG 3350, 5% v/v Jeffamine M-600 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.896 α = 90 b = 101.847 β = 90 c = 170.095 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 270 2019-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
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 2.63 48.83 100 0.146 0.156 0.055 0.998 12.3 8 42052
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 2.63 2.73 100 2.609 2.783 0.964 0.441 8.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.63 48.78 39931 2056 99.93 0.2338 0.231 0.2323 0.2884 0.2863 RANDOM 62.835
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] 3.68 0.12 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_3_deg 15.375 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_1_deg 6.941 r_angle_refined_deg 1.43 r_angle_other_deg 1.233 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_3_deg 15.375 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_1_deg 6.941 r_angle_refined_deg 1.43 r_angle_other_deg 1.233 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8431 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxDC data collection XDS data reduction Aimless data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction