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The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotin and ADP
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 MICROBATCH 5.2 295 PEG20K, Acetate, NaOH, 2.5mM ADP, 2.5mM Biotin, 1mM MnCl2, pH 5.2, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.001 α = 90 b = 72.718 β = 90 c = 104.21 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2005-06-23 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 1.95 50 98.6 0.124 0.097 7.3 5.5 39486 38943 26.22
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 1.95 2.02 99.3 0.486 0.395 4.1 5.9 3873
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 2FYK 1.95 36.24 39486 38943 1940 98.6 0.24 0.24 0.24 0.2404 0.269 0.2682 RANDOM 35.1
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] -4.61 7.14 -2.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_angle_deg 1.2 c_improper_angle_d 0.81 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3674 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 66
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing