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Kineococcus siccus GH5_7 Mannanase, Apo
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 293 100 mM EPPS pH 8.9, 200 mM MgCl2, 22.5% PEG3350. 2mg/ml 2P+1ML
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.933 α = 90 b = 75.612 β = 90 c = 99.625 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 2024-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 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 1.547 60.23 93.1 0.231 0.245 0.995 7.1 9.5 37814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.547 1.716 58.9 1.389 0.636
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 1.547 60.23 35916 1898 69.02 0.15563 0.15423 0.1533 0.18183 0.1798 RANDOM 15.81
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] 0.14 -0.16 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 7.48 r_dihedral_angle_2_deg 5.826 r_long_range_B_refined 5.417 r_long_range_B_other 4.716 r_scangle_other 2.592 r_scbond_it 1.635 r_scbond_other 1.635 r_mcangle_it 1.627 r_mcangle_other 1.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 7.48 r_dihedral_angle_2_deg 5.826 r_long_range_B_refined 5.417 r_long_range_B_other 4.716 r_scangle_other 2.592 r_scbond_it 1.635 r_scbond_other 1.635 r_mcangle_it 1.627 r_mcangle_other 1.627 r_mcbond_it 1.061 r_mcbond_other 1.047 r_angle_refined_deg 0.89 r_angle_other_deg 0.345 r_chiral_restr 0.049 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing