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X-ray structure of PSmOrange3 (trigonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Na/K Phosphate
Crystal Properties Matthews coefficient Solvent content 5.61 78.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.165 α = 90 b = 137.165 β = 90 c = 55.223 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 EIGER X 16M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 68.59 100 0.98 6.3 19.1 15169
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.94 0.7
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 2.8 68.59 14009 651 93.599 0.18 0.1783 0.1854 0.2099 0.1857 55.401
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] -0.164 -0.082 -0.164 0.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.684 r_dihedral_angle_3_deg 20.469 r_dihedral_angle_4_deg 18.965 r_lrange_other 14.917 r_lrange_it 14.911 r_scangle_it 11.677 r_scangle_other 11.673 r_dihedral_angle_1_deg 8.32 r_scbond_it 7.599 r_scbond_other 7.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.684 r_dihedral_angle_3_deg 20.469 r_dihedral_angle_4_deg 18.965 r_lrange_other 14.917 r_lrange_it 14.911 r_scangle_it 11.677 r_scangle_other 11.673 r_dihedral_angle_1_deg 8.32 r_scbond_it 7.599 r_scbond_other 7.596 r_mcangle_it 6.625 r_mcangle_other 6.624 r_mcbond_it 4.551 r_mcbond_other 4.485 r_angle_refined_deg 2.193 r_angle_other_deg 1.347 r_nbd_refined 0.208 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.185 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.159 r_symmetry_nbtor_other 0.105 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_symmetry_nbd_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1715 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing