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Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-unbound 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 6.2 298 7% PEG 20000, 0.1M Mes-NaOH, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.43 α = 90 b = 127.82 β = 90 c = 133.8 γ = 90
Symmetry Space Group P 21 21 21
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 2009-06-26 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 2.38 100 99.5 0.083 27.2 6.9 71995 71995 34.6
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 2.38 2.47 96.3 0.409 2.5 4.8 6885
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 2.38 29.96 2 69778 69778 3534 96.4 0.232 0.232 0.2369 0.271 0.2743 RANDOM 57.5
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] 6.26 16.04 -22.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 3.13 c_mcangle_it 2.65 c_scbond_it 2.06 c_mcbond_it 1.55 c_angle_deg 1.1 c_improper_angle_d 0.72 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 3.13 c_mcangle_it 2.65 c_scbond_it 2.06 c_mcbond_it 1.55 c_angle_deg 1.1 c_improper_angle_d 0.72 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 9682 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 48
Software Software Software Name Purpose BSS data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling