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Mutant I253M 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 5.5 295 3.85M Na Formate, 0.1M Acetate, 1mM DTT, pH 5.5, Microbach, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.24 62.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.983 α = 90 b = 104.983 β = 90 c = 139.577 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 V Mirror 2006-09-06 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 2.2 20 100 0.07 0.069 11 13.8 40184 40184 35
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 2.2 2.28 100 0.503 0.488 4.6 13.9
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 2.2 19.75 40184 40184 1996 100 0.201 0.201 0.202 0.221 0.223 RANDOM 40.1
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] -0.93 -0.93 1.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.17 c_scbond_it 2.16 c_mcangle_it 2.08 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4172 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 27
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing