☰ Navigation Tabs
Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.05 M imidazole and 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5, 20% (v/v) ethylene glycol, 10% (w/v) polyethylene glycol 8000, 0.02 M ethylenediaminetetraacetic acid disodium salt
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.324 α = 90 b = 149.755 β = 103.57 c = 105.671 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 80 PIXEL DECTRIS EIGER X 9M 2017-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97872 APS 21-ID-D
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 1.95 102.7 95.9 17.1 6.3 125182
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 1.95 1.98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 25 118511 6274 95.83 0.19702 0.19485 0.1966 0.23736 0.2399 RANDOM 35.968
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] 2.36 0.48 -0.96 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_3_deg 15.663 r_dihedral_angle_4_deg 15.445 r_long_range_B_refined 6.805 r_dihedral_angle_1_deg 6.144 r_mcangle_it 2.427 r_scbond_it 2.044 r_mcbond_it 1.517 r_angle_refined_deg 1.381 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_3_deg 15.663 r_dihedral_angle_4_deg 15.445 r_long_range_B_refined 6.805 r_dihedral_angle_1_deg 6.144 r_mcangle_it 2.427 r_scbond_it 2.044 r_mcbond_it 1.517 r_angle_refined_deg 1.381 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12760 Nucleic Acid Atoms Solvent Atoms 962 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction autoPROC data scaling PHENIX phasing