☰ Navigation Tabs
Crystal structure of YgiN in complex with menadione
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 sodium citrate, ammonium sulfate, sodium/potassium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.562 α = 90 b = 102.562 β = 90 c = 102.562 γ = 90
Symmetry Space Group P 41 3 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 ADSC QUANTUM 210 2004-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9788 NSLS X6A
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 1.69 50 100 0.07 0.07 50 8 19783 19783 2 2
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 1.69 1.77 99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION direct input of native model THROUGHOUT 1.7 25.65 19783 19783 1056 100 0.20949 0.20949 0.20756 0.24904 0.2344 RANDOM 22.765
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 r_scangle_it 6.428 r_dihedral_angle_1_deg 6.102 r_scbond_it 4.137 r_mcangle_it 2.379 r_angle_refined_deg 2 r_mcbond_it 1.337 r_angle_other_deg 1.02 r_symmetry_vdw_other 0.4 r_symmetry_vdw_refined 0.284 r_nbd_other 0.261
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.428 r_dihedral_angle_1_deg 6.102 r_scbond_it 4.137 r_mcangle_it 2.379 r_angle_refined_deg 2 r_mcbond_it 1.337 r_angle_other_deg 1.02 r_symmetry_vdw_other 0.4 r_symmetry_vdw_refined 0.284 r_nbd_other 0.261 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.235 r_symmetry_hbond_refined 0.223 r_chiral_restr 0.13 r_nbtor_other 0.092 r_bond_refined_d 0.024 r_gen_planes_other 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 797 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing