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Crystal structure of Gilliamella bombicola lactate deydrogenase (GbLDH)
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, SITTING DROP 294 0.1 M Tris pH 7.0 -7.5 10-12% PEG3350 and 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.229 α = 100.42 b = 93.559 β = 91.82 c = 192.842 γ = 90.19
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 PILATUS3 6M 2024-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 2.2 49.24 92.8 0.161 0.194 0.105 0.871 6.3 3.3 301715
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 2.2 2.24 54.9 0.358 0.44 0.251 0.211 2.9
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 2.2 49.24 286536 15087 75.16 0.23093 0.23004 0.2313 0.24785 0.249 RANDOM 3.488
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] 1.13 3.31 -1.27 1.98 -2.27 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.892 r_dihedral_angle_2_deg 7.878 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 1.601 r_long_range_B_other 1.601 r_angle_refined_deg 1.545 r_mcangle_it 1.002 r_mcangle_other 1.002 r_scangle_other 0.693 r_mcbond_it 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.892 r_dihedral_angle_2_deg 7.878 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 1.601 r_long_range_B_other 1.601 r_angle_refined_deg 1.545 r_mcangle_it 1.002 r_mcangle_other 1.002 r_scangle_other 0.693 r_mcbond_it 0.63 r_mcbond_other 0.63 r_angle_other_deg 0.591 r_scbond_it 0.437 r_scbond_other 0.437 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 44000 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 496
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction