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Mutant Y29M structure of PH0725 from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WNG PDB entry 1WNG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbach 6.5 295 1.8M Ammonium Sulfate, 0.1M MES, 0.01M Co Chloride, 1mM DTT, pH 6.5, Microbach, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.697 α = 90 b = 104.697 β = 90 c = 136.615 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Mirror 2006-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 15 100 0.096 0.095 9.2 13.8 26782 26782 54.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.438 0.425 4.9 13.2
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 (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 1WNG 2.5 14.9 26782 26782 1343 100 0.19 0.19 0.1904 0.237 0.2372 RANDOM 42.9
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] -3.07 -3.07 6.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.15 c_mcangle_it 2.16 c_scbond_it 2.08 c_angle_deg 1.4 c_mcbond_it 1.29 c_improper_angle_d 0.91 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4164 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 69
Software Software Software Name Purpose CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing