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Crystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8Q PDB entry 1L8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.6M LITHIUM SULFATE, 0.05M MAGNESIUM SULFATE, 0.05M Na-HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 221.817 α = 90 b = 221.817 β = 90 c = 55.602 γ = 120
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 ADSC QUANTUM 315 monochromator 2004-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.95 50 96.3 0.078 13.4 10.4 11053 10640
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) 2.95 3.06 74.6 0.351 2.5 3.7 812
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1L8Q 3 48.12 10546 10290 1057 97.6 0.291 0.234 0.233 0.2278 0.291 0.2812 random
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_angle_deg 1.36 c_improper_angle_d 0.966 c_bond_d 0.00838
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1939 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling