☰ Navigation Tabs
The N-terminal domain of riboflavin synthase in complex with riboflavin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I8D PDB entry 1I8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 70 mM sodium potassium phosphate, pH 7.0, 100 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.161 α = 90 b = 104.383 β = 90 c = 85.113 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2000-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8424 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 99.4 7171 7131
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.63 100
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 PDB entry 1I8D 2.6 19.7 7131 6793 337 99.46 0.17699 0.17699 0.17409 0.165 0.23469 0.2135 RANDOM 38.393
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] -1.58 2.17 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.087 r_scangle_it 5.286 r_scbond_it 3.216 r_mcangle_it 2.151 r_angle_refined_deg 1.798 r_mcbond_it 1.068 r_symmetry_vdw_refined 0.318 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.087 r_scangle_it 5.286 r_scbond_it 3.216 r_mcangle_it 2.151 r_angle_refined_deg 1.798 r_mcbond_it 1.068 r_symmetry_vdw_refined 0.318 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.112 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1330 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing