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Crystal structure of P123A_Msd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M MES pH 6.4, 0.2M Mg-acetate tetrahydrate, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.66 α = 90 b = 108.56 β = 90 c = 53.19 γ = 90
Symmetry Space Group P 21 21 2
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 6M 2021-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.56 19.763 100 0.99 16.79 12.5 53097
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 1.562 1.602 0.83
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 1.562 19.763 53016 967 99.896 0.171 0.1703 0.1829 0.1932 0.2053 18.634
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] -0.006 -0.023 0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.976 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_2_deg 9.213 r_dihedral_angle_1_deg 5.809 r_lrange_it 5.732 r_lrange_other 5.671 r_scangle_it 4.518 r_scangle_other 4.517 r_scbond_it 3.063 r_scbond_other 3.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.976 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_2_deg 9.213 r_dihedral_angle_1_deg 5.809 r_lrange_it 5.732 r_lrange_other 5.671 r_scangle_it 4.518 r_scangle_other 4.517 r_scbond_it 3.063 r_scbond_other 3.062 r_mcangle_other 2.465 r_mcangle_it 2.46 r_angle_refined_deg 1.746 r_mcbond_it 1.653 r_mcbond_other 1.632 r_angle_other_deg 0.664 r_symmetry_xyhbond_nbd_refined 0.257 r_nbd_refined 0.22 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.181 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.133 r_metal_ion_refined 0.116 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_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 2390 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing