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Cytosolic Malate Dehydrogenase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 283 0.18 M ammonium sulfate, 0.09 M sodium acetate trihydrate, 27% polyethylene glycol monomethyl ether 2000, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.66 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.592 α = 90 b = 118.545 β = 90 c = 148.219 γ = 90
Symmetry Space Group P 2 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 RIGAKU SATURN 944+ 2015-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541870
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 1.8 43.67 94.42 0.1717 0.186 0.07035 0.985 10.15 6.7 110856
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) 1 0.864 1.8 67.49 1.072 1.252 0.6292 0.454 1.3 3.7
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4MDH 1.8 43.67 95355 94.5 0.1895 0.3142 0.1881
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7409 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing