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Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 Complexed with ATP and Biotin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 295 PEG20K, Acetate, NaOH, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.251 α = 90 b = 82.85 β = 101.78 c = 72.661 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 CCD MARRESEARCH MIRRORS 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
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 1.5 40 98.3 0.054 0.042 18 3.3 70918 69713 16.9
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 1.5 1.55 89.1 0.34 0.302 2.2 2.7 6312
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 FOURIER SYNTHESIS THROUGHOUT 2FYK 1.5 32.68 70918 69713 3546 98.3 0.192 0.192 0.192 0.1919 0.207 0.2075 RANDOM 22.7
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] -1.39 -0.27 -3.5 4.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_angle_deg 1.2 c_improper_angle_d 0.89 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3674 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 94
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing