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Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.507 α = 90 b = 126.002 β = 90 c = 83.942 γ = 90
Symmetry Space Group C 2 2 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 PIXEL PSI PILATUS 6M 2015-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.987 APS 24-ID-C
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 2.2 50 95.4 0.062 0.068 0.027 9.6 5.3 31361 31.7
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 2.2 2.24 58.3 0.379 0.449 0.235 0.745 1.55 2.7 937
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RR2 2.21 49.48 30821 1532 93.3 0.223 0.2158 0.258 0.2463 RANDOM 63.8
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] 8.81 7.28 -16.09
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.9 c_scangle_it 6.55 c_scbond_it 4.93 c_mcangle_it 4.78 c_mcbond_it 3.19 c_improper_angle_d 1.8 c_angle_deg 1.4 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3035 Nucleic Acid Atoms 721 Solvent Atoms 65 Heterogen Atoms 18
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data scaling CNS refinement PDB_EXTRACT data extraction HKL-3000 data reduction