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Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GUZ MDH WITH PDB-CODE 1GUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 ~20 MG/ML, 50 MM TRIS-HCL, PH 7.4, 40 % PEG-MME5000, 100 MM
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.425 α = 90 b = 85.824 β = 104.61 c = 117.498 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.5 19.92 92.5 0.079 11 2.8 37824 19.6
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 2.5 2.59 84.1 0.251 2.5
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 MDH WITH PDB-CODE 1GUZ 2.5 19.92 37824 3815 88 0.216 0.216 0.208 0.305 0.292 RANDOM 28.3
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.01 c_mcangle_it 2.43 c_scbond_it 1.97 c_mcbond_it 1.44 c_angle_deg 1.3 c_improper_angle_d 0.91 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.01 c_mcangle_it 2.43 c_scbond_it 1.97 c_mcbond_it 1.44 c_angle_deg 1.3 c_improper_angle_d 0.91 c_bond_d 0.007 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 8945 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing