☰ Navigation Tabs
Kineococcus siccus GH5_7 Mannanase, AMPD bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ESMfold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Spermine, Spermidine, Diaminobutatne, DL-Ornithine 10 mM each. AMPD, GlyGly 50 mM each pH 8.5, 10% PEG 8000, 20% 1,5-Pentanediol
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.946 α = 90 b = 76.157 β = 90 c = 101.47 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 EIGER2 X 16M 2023-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.418 76.16 99.9 0.085 0.092 0.998 12.81 7.58 72481
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 99.4 0.535 0.576 2.68 7.19
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.418 60.91 72481 2000 99.862 0.132 0.1314 0.1307 0.157 0.1568 16.176
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] -1.379 -0.111 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 11.33 r_dihedral_angle_2_deg 9.914 r_dihedral_angle_1_deg 6.842 r_lrange_it 5.502 r_lrange_other 5.418 r_dihedral_angle_other_3_deg 4.771 r_scangle_it 2.925 r_scangle_other 2.924 r_scbond_it 1.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 11.33 r_dihedral_angle_2_deg 9.914 r_dihedral_angle_1_deg 6.842 r_lrange_it 5.502 r_lrange_other 5.418 r_dihedral_angle_other_3_deg 4.771 r_scangle_it 2.925 r_scangle_other 2.924 r_scbond_it 1.934 r_scbond_other 1.933 r_mcangle_it 1.676 r_mcangle_other 1.675 r_angle_refined_deg 1.231 r_mcbond_it 1.096 r_mcbond_other 1.083 r_angle_other_deg 0.452 r_symmetry_xyhbond_nbd_other 0.384 r_xyhbond_nbd_refined 0.248 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.189 r_nbd_other 0.185 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing