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Crystal structure of biphenyl synthase from Malus domestica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 278 14% PEG 8000, 0.3M Ammonium acetate, 0.1M sodium-HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.27 α = 90 b = 113.02 β = 93.15 c = 62.77 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 ADSC QUANTUM 315 mirrors 2010-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.99980 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.173 62.675 98.3 0.084 0.094 0.041 11.3 4.5 251517 7.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.173 1.24 94.2 0.297 0.297 0.378 0.231 1.4 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BI5 1.173 27.917 1.35 251383 12622 98.21 0.0992 0.0981 0.1036 0.1216 0.1024 12.9143
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.424 f_angle_d 1.421 f_chiral_restr 0.087 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5919 Nucleic Acid Atoms Solvent Atoms 1171 Heterogen Atoms 32
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction