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Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDN PDB ENTRY 1LDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 298 6%(w/v) PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.77 α = 90 b = 123.54 β = 107.75 c = 85.79 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 CCD RAYONIX MX-225 2010-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 100 97.3 0.107 8.2 2.9 57963 57963 14.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 97.4 0.413 2.4 2.8 8475
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1LDN 2.3 29.67 2 55635 55635 2829 93.1 0.195 0.195 0.2018 0.246 0.2477 RANDOM 33.3
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] 24.47 6.65 -15.71 -8.75
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.93 c_mcangle_it 2.03 c_scbond_it 2.02 c_mcbond_it 1.26 c_angle_deg 1.2 c_improper_angle_d 0.73 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.93 c_mcangle_it 2.03 c_scbond_it 2.02 c_mcbond_it 1.26 c_angle_deg 1.2 c_improper_angle_d 0.73 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9655 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 234
Software Software Software Name Purpose BSS data collection MOLREP phasing CNS refinement MOSFLM data reduction SCALA data scaling