☰ Navigation Tabs
Crystal structure of D-lactate dehydrogenase from Lacticaseibacillus rhamnosus in its apoform
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.326 α = 90 b = 80.25 β = 110.85 c = 70.225 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 100 PIXEL DECTRIS EIGER2 X 16M 2025-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.97918 SSRF BL17UM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 48.59 99.4 0.367 0.398 0.152 0.985 3.5 6.9 39444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.7 2.818 3.045 1.144 0.429 7
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 2.1 48.59 37410 1937 99.21 0.25267 0.24916 0.2489 0.32382 0.3241 RANDOM 34.119
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] -3.09 -4.13 3.28 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.209 r_dihedral_angle_3_deg 17.229 r_dihedral_angle_4_deg 16.726 r_dihedral_angle_1_deg 8.557 r_long_range_B_refined 8.262 r_long_range_B_other 8.262 r_scangle_other 6.331 r_mcangle_it 5.975 r_mcangle_other 5.975 r_scbond_it 4.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.209 r_dihedral_angle_3_deg 17.229 r_dihedral_angle_4_deg 16.726 r_dihedral_angle_1_deg 8.557 r_long_range_B_refined 8.262 r_long_range_B_other 8.262 r_scangle_other 6.331 r_mcangle_it 5.975 r_mcangle_other 5.975 r_scbond_it 4.356 r_scbond_other 4.355 r_mcbond_it 4.165 r_mcbond_other 4.163 r_angle_refined_deg 2.063 r_angle_other_deg 1.374 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5092 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing