☰ Navigation Tabs
Crystal structure of Ni2+ dependent glycerol-1-phosphate dehydrogenase AraM from Bacillus subtilis
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 8.2 293 20.0-25.5% (w/v) PEG 3350, 0.15-0.29 M KSCN
Crystal Properties Matthews coefficient Solvent content 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.015 α = 90 b = 70.499 β = 95.51 c = 72.609 γ = 90
Symmetry Space Group C 1 2 1
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 4M 2022-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.95 45.51 98.4 0.978 8 1.9 9676
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 2.95 3.13 0.433
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 2.95 43.036 9674 512 98.114 0.245 0.2406 0.2481 0.3102 0.3109 71.254
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] -1.805 -0.435 -0.747 2.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.946 r_dihedral_angle_6_deg 15.495 r_dihedral_angle_2_deg 11.316 r_lrange_other 8.932 r_lrange_it 8.931 r_dihedral_angle_1_deg 6.267 r_scangle_it 5.21 r_scangle_other 5.209 r_mcangle_it 5.078 r_mcangle_other 5.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.946 r_dihedral_angle_6_deg 15.495 r_dihedral_angle_2_deg 11.316 r_lrange_other 8.932 r_lrange_it 8.931 r_dihedral_angle_1_deg 6.267 r_scangle_it 5.21 r_scangle_other 5.209 r_mcangle_it 5.078 r_mcangle_other 5.077 r_scbond_it 3.185 r_scbond_other 3.184 r_mcbond_it 3.16 r_mcbond_other 3.16 r_angle_refined_deg 1.509 r_dihedral_angle_other_2_deg 1.312 r_angle_other_deg 0.517 r_nbd_other 0.255 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.168 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_metal_ion_refined 0.03 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3027 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing