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Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in complex with oxamate, NADH and FBP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18.5 % peg 3350
0.24 M sodium malonate dibasic monohydrate
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.369 α = 90 b = 111.504 β = 99.78 c = 101.793 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 PILATUS 2M 2022-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.616 100.314 99.3 0.1946 0.222 0.105 0.983 5.62 4.31 46537
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) 2.616 2.661 100 0.7544 0.8525 0.3914 0.726 1.99 4.56 2342
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 (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 4ojn 2.616 100.31 46528 2317 99.3 0.1884 0.1862 0.1783 0.2318 0.2227 RANDOM 39.64
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] 15.5699 0.3017 -8.3056 -7.2643
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.55 t_omega_torsion 2.85 t_angle_deg 0.93 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9900 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 240
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling TRUNCATE data processing BUSTER refinement BUSTER refinement PHENIX phasing