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STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. THE STRUCTURE OF SORGHUM NADP-MALATE DEHYDROGENASE IN ITS OXIDIZED FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.74 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.424 α = 90 b = 153.944 β = 90 c = 160.042 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MAR scanner 345 mm plate 1998-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 50 94.9 0.068 10.8 5.2 66459 30.2
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 2.4 2.44 99.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BMD 2.4 50 66489 2010 94.9 0.221 0.2206 0.271 0.2698 RANDOM 40.3
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] 1.06 -1.6 0.53
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 22.8 x_angle_deg 2.1 x_improper_angle_d 0.93 x_bond_d 0.249 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 22.8 x_angle_deg 2.1 x_improper_angle_d 0.93 x_bond_d 0.249 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10850 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement