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Crystal structure of NAD(H)-dependent malate dehydrogenase complexed with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Malate Dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.29 α = 90 b = 85.16 β = 90 c = 118.07 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 ADSC QUANTUM 210 2005-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.978 Photon Factory AR-NW12A
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 2.08 69.07 90.9 47323 43032 2 2 17.8
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 2.08 2.21
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 Malate Dehydrogenase 2.08 40.06 47323 42931 2111 99.7 0.208 0.208 0.1881 0.247 0.1868 RANDOM 27.8
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] -3.6 3.53 0.06
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 3.65 c_scbond_it 2.52 c_mcangle_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.17 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4978 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 110
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing