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Crystal Structure of L-lactate dehydrogenase from Cyprinus carpio
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 277 100mM Tris-HCl (pH8.5), 17.5% trehalose, 30% PEG8000, 100mM NaSCN, MICROBATCH, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.56 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.2 α = 90 b = 156.2 β = 90 c = 84.3 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 4 2003-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 46.2 96.5 96.5 46153 44544 -3 24.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.44 89.7 89.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6ldh 2.3 46.2 46153 44544 4489 95.5 0.2 0.2 0.2052 0.238 0.242 RANDOM 39.7
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] -8.77 -8.77 17.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 2.98 c_scbond_it 2.07 c_mcangle_it 1.87 c_angle_deg 1.3 c_mcbond_it 1.18 c_improper_angle_d 0.81 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5070 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 92
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing