☰ Navigation Tabs
Crystal Structure of Riboflavin Lyase (RcaE) with cofactor FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9O PDB ENTRY 3B9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Bis-Tris-HCl, 45% polypropylene glycol P400
Crystal Properties Matthews coefficient Solvent content 2.53 51.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.25 α = 90 b = 113.47 β = 90 c = 117.81 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 PIXEL DECTRIS PILATUS3 6M 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 64.01 99.2 0.14 13.9 18.6 81065 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.9 97.8 1.75 18.6
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 PDB ENTRY 3B9O 1.9 64.01 1.33 81065 4121 99.9 0.158 0.156 0.159 0.194 0.1944
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 17.034 f_angle_d 1.017 f_chiral_restr 0.058 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6910 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction PHENIX model building iMOSFLM data scaling PHENIX phasing