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Crystal Structure of a DiB2-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 10% 0.1 M iron(III) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.241 α = 90 b = 68.241 β = 90 c = 216.292 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 CCD MARMOSAIC 300 mm CCD 2018-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 2.02 72.1 100 0.099 0.033 11.5 8.8 39425 30.423
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 2.02 2.05 97.5 0.989 0.335 2.1 7.9
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 2.02 72.1 37418 1885 99.72 0.2071 0.2051 0.2145 0.2479 0.2541 RANDOM 36.833
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] 0.21 0.11 0.21 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.997 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 15.604 r_dihedral_angle_1_deg 7.494 r_mcangle_it 4.284 r_mcbond_other 3.214 r_mcbond_it 3.212 r_angle_other_deg 2.337 r_angle_refined_deg 1.689 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.997 r_dihedral_angle_4_deg 21.805 r_dihedral_angle_3_deg 15.604 r_dihedral_angle_1_deg 7.494 r_mcangle_it 4.284 r_mcbond_other 3.214 r_mcbond_it 3.212 r_angle_other_deg 2.337 r_angle_refined_deg 1.689 r_chiral_restr 0.082 r_bond_other_d 0.035 r_gen_planes_other 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3698 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing PDB_EXTRACT data extraction xia2 data reduction