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Crystal Structure Of The Biotin Protein Ligase (Mutation R48A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DZC PDB ENTRIES 2DZC AND 2D5D experimental model PDB 2D5D PDB ENTRIES 2DZC AND 2D5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.96 295 10.5w/v(%) PEG 20000, 0.1M Acet, NaOH, 2.5M Biotin, 2.5M ATP, pH 4.96, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.572 α = 90 b = 63.487 β = 93.65 c = 74.715 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 2006-11-25 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 2.71 49.27 91.1 0.107 0.093 6.7 3.1 16349 55.7
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 2.7 2.8 86.6 0.32 0.284 2.03 2.8 1378
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 ENTRIES 2DZC AND 2D5D 2.71 38.93 17941 16349 835 91 0.216 0.216 0.2155 0.273 0.2732 RANDOM 43.1
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] -5.71 3.49 -3.92 9.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 3.15 c_mcangle_it 2.429 c_scbond_it 1.999 c_mcbond_it 1.402 c_angle_deg 1.4 c_improper_angle_d 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.1 c_scangle_it 3.15 c_mcangle_it 2.429 c_scbond_it 1.999 c_mcbond_it 1.402 c_angle_deg 1.4 c_improper_angle_d 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4595 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling