☰ Navigation Tabs
Putative BLF1-like Deamidase from Methylomonas sp. Kb3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M MES monohydrate, pH 6.5,1.6 M Magnesium sulfate heptahydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.647 α = 90 b = 168.647 β = 90 c = 168.647 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 PIXEL DECTRIS EIGER X 16M 2025-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.95 46.818 100 1 24.5 44.8 59984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.722
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 1.95 46.818 59975 3019 99.977 0.161 0.1601 0.1602 0.1763 0.1761 RANDOM 43.744
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_lrange_it 19.217 r_lrange_other 18.27 r_dihedral_angle_2_deg 16.665 r_scangle_it 15.922 r_scangle_other 15.508 r_dihedral_angle_6_deg 14.107 r_scbond_it 12.324 r_mcangle_it 11.971 r_mcangle_other 11.967 r_scbond_other 11.932
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.217 r_lrange_other 18.27 r_dihedral_angle_2_deg 16.665 r_scangle_it 15.922 r_scangle_other 15.508 r_dihedral_angle_6_deg 14.107 r_scbond_it 12.324 r_mcangle_it 11.971 r_mcangle_other 11.967 r_scbond_other 11.932 r_dihedral_angle_3_deg 11.617 r_mcbond_it 9.548 r_mcbond_other 9.547 r_dihedral_angle_1_deg 7.089 r_rigid_bond_restr 5.07 r_angle_refined_deg 2.047 r_angle_other_deg 0.666 r_symmetry_xyhbond_nbd_refined 0.363 r_nbd_refined 0.205 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.177 r_nbd_other 0.175 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.026 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1694 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing