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Structure of berberine bridge enzyme, C166A variant in complex with (S)-reticuline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 0.2 M MAGNESIUMCHLORIDE, 30% PEG-4000, 0.1 M TRIS/HCL, pH 8.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.87 α = 90 b = 68.87 β = 90 c = 246.46 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 CCD MARMOSAIC 225 mm CCD 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9794 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.496 41.9 97.4 0.053 16.6 8.4 95673 95673 12.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 91.5 0.233 5.1 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3d2j 1.496 41.892 1.99 95673 95673 4780 98.83 0.162 0.162 0.162 0.1582 0.177 0.1741 random 18.992
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] -1.854 -1.854 -1.466
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.276 f_angle_d 1.065 f_chiral_restr 0.067 f_bond_d 0.013 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3925 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction XSCALE data scaling PHASER phasing