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Crystal structure of human primosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QCL 4QCL, 4Q5V, 4RR2, 4Y97 experimental model PDB 4Q5V 4QCL, 4Q5V, 4RR2, 4Y97 experimental model PDB 4RR2 4QCL, 4Q5V, 4RR2, 4Y97 experimental model PDB 4Y97 4QCL, 4Q5V, 4RR2, 4Y97
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.2 M lithium sulphate, 50 mM TRIS HCl pH 8.5, 2 mM TCEP pH 7.5, 11.2% w/v PEG 4,000, 3% v/v ethanol, 0.5% v/v polypropylene glycol P400 and 0.2 mM EDTA
Crystal Properties Matthews coefficient Solvent content 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.096 α = 90 b = 210.164 β = 93.56 c = 172.565 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 PILATUS 6M-F 2013-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.6 50 80.5 0.063 12.2 2.6 74238 -1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.66 72.7 0.364 1.93 1.9 3348
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4QCL, 4Q5V, 4RR2, 4Y97 3.6 39.94 1 64105 3215 68.9 0.268 0.2763 0.326 0.3273 RANDOM 61.2
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] 1.91 2.94 -5.74 3.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 7.41 c_mcangle_it 6.67 c_scbond_it 4.76 c_mcbond_it 3.97 c_angle_deg 1.8 c_improper_angle_d 1.19 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37642 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling CNS phasing CNS refinement PDB_EXTRACT data extraction