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Crystal Structure of Mannitol Dehydrogenase (ChMDH) from Cladosporium herbarum in complex with NADP+ and Na
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 25% PEG 1500, 100 mM sodium propionate/sodium cacodylate/BIS-TRIS propane (2:1:2 molar ratio), pH 7, 5 mM NADP+
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.867 α = 90 b = 119.322 β = 94.884 c = 111.211 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 ADSC QUANTUM 315 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.0379 50 97.6 0.087 0.137 16.6 2.9 141106 27.8196736865
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.0379 2.09 0.656
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3GDF 2.03797368098 31.4045238396 1.3435622572 141045 1990 95.8485668076 0.154547684041 0.154135383197 0.1546 0.182916664342 0.1833 32.9031283964
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 f_dihedral_angle_d 4.93040445067 f_angle_d 0.828817897269 f_chiral_restr 0.0508401352847 f_bond_d 0.00703664459293 f_plane_restr 0.0041607803175
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15923 Nucleic Acid Atoms Solvent Atoms 1414 Heterogen Atoms 388
Software Software Software Name Purpose PHENIX refinement PHENIX refinement SBC-Collect data collection Coot model building HKL-3000 data scaling PHASER phasing HKL-3000 data reduction