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Crystal Structure of the DiB-RM-split Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QWD PDB entry 1QWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 1.6 M ammonium sulfate, 0.1 M MES, pH 4.5, supplemented with 0.5% n-Dodecyl-b-D-maltoside
Crystal Properties Matthews coefficient Solvent content 2.8 56.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.146 α = 90 b = 57.146 β = 90 c = 138.63 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 225 mm CCD 2020-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.33 46.21 100 0.087 0.03 10.9 8 10501 49.674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.37 100 0.697 0.286 1.8 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1QWD 2.33 44.13 9939 501 99.9 0.2404 0.2385 0.2482 0.2787 0.2813 RANDOM 55.752
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] 0.53 0.53 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.49 r_dihedral_angle_4_deg 20.018 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 8.139 r_mcangle_it 6.253 r_mcbond_it 4.349 r_mcbond_other 4.348 r_angle_other_deg 2.344 r_angle_refined_deg 1.547 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.49 r_dihedral_angle_4_deg 20.018 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 8.139 r_mcangle_it 6.253 r_mcbond_it 4.349 r_mcbond_other 4.348 r_angle_other_deg 2.344 r_angle_refined_deg 1.547 r_chiral_restr 0.069 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1218 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOLREP phasing xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction