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Crystal structure of Trimucrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7X4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.3M Zinc acetate, 25% PEG 3350, 0.1M Cacodylate, 5% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.954 α = 90 b = 58.397 β = 90.266 c = 42.871 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97625 NSRRC TPS 07A
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 1.68 30 99.6 0.996 10.6 4.6 15133
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 1.68 1.78 0.836
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 1.68 29.22 15132 752 99.572 0.176 0.1739 0.184 0.2171 0.2251 20.981
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] -0.523 -0.236 1.165 -0.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.237 r_dihedral_angle_4_deg 18.739 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 7.146 r_lrange_it 5.848 r_lrange_other 5.848 r_scangle_it 3.961 r_scangle_other 3.959 r_mcangle_it 2.879 r_mcangle_other 2.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.237 r_dihedral_angle_4_deg 18.739 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 7.146 r_lrange_it 5.848 r_lrange_other 5.848 r_scangle_it 3.961 r_scangle_other 3.959 r_mcangle_it 2.879 r_mcangle_other 2.876 r_scbond_it 2.528 r_scbond_other 2.526 r_mcbond_it 1.81 r_mcbond_other 1.674 r_angle_refined_deg 1.449 r_angle_other_deg 1.338 r_nbd_refined 0.229 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_refined 0.186 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.16 r_nbd_other 0.156 r_nbtor_refined 0.153 r_metal_ion_refined 0.084 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1042 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing