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Crystal Structure of endonuclease IV from Geobacillus kaustophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XP3 PDB ENTRY 1XP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M cacodylate, 30% polyethylene glycol 600, 1M NaCl, 10% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.17 α = 90 b = 85.17 β = 90 c = 140.22 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD MARMOSAIC 225 mm CCD 2007-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000000 SPring-8 BL26B2
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 1.6 50 99.7 0.049 64.904 14.9 40267 -3
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 1.6 1.66 97.6 0.216 6.6 3860
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 PDB ENTRY 1XP3 1.6 23.42 39270 3948 97.3 0.197 0.1909 0.222 0.2167 RANDOM 17.605
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] -0.49 -0.27 -0.49 0.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 3.35 c_scbond_it 2.39 c_mcangle_it 1.71 c_angle_deg 1.6 c_improper_angle_d 1.52 c_mcbond_it 1.15 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2316 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction BSS data collection HKL-2000 data reduction HKL-2000 data scaling