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Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y395L mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DTZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 100 mM TRIS 8.5, 40-60% MPD
Crystal Properties Matthews coefficient Solvent content 1.86 34.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.462 α = 90 b = 50.83 β = 90 c = 90.175 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 2017-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.83 30 95.6 0.084 0.099 0.053 10.7 3.3 29372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.9 85.6 0.38 0.462 0.258 0.876 2.6
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 6DTZ 1.82 29.28 15173 847 97 0.276 0.2734 0.2812 0.3241 0.3258 RANDOM 54.126
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] 11.21 -5.46 -5.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 20.491 r_dihedral_angle_3_deg 16.152 r_dihedral_angle_1_deg 6.343 r_angle_other_deg 1.313 r_angle_refined_deg 1.156 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 20.491 r_dihedral_angle_3_deg 16.152 r_dihedral_angle_1_deg 6.343 r_angle_other_deg 1.313 r_angle_refined_deg 1.156 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1431 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction