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Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NWQ PDB ENTRY 2NWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10% v/v MPD, 24% w/v PEG4000, 0.1 M ammonium thiocyanate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.39 α = 90 b = 87.25 β = 112.98 c = 83.81 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 93 CCD RIGAKU SATURN 944+ Osmic VariMax Cu-HF optics 2010-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.36 77.161 99.9 0.135 6.3 4.06 45068 44993 26.5
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 2.36 2.44 99.8 0.489 2 3.66 4449
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2NWQ 2.6 40.949 1.33 33738 1668 99.82 0.1913 0.1885 0.1789 0.2449 0.2363 RANDOM 26.2043
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] -3.3431 1.3314 4.3966 -1.0535
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.837 f_angle_d 1.28 f_chiral_restr 0.078 f_bond_d 0.011 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8252 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 192
Software Software Software Name Purpose d*TREK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction