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Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the absence of copper from Synechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20%(v/v) PEG3350, 0.2M magnesium acetate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.042 α = 90 b = 146.887 β = 90 c = 161.879 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 2009-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 3.3 50 89 0.147 22942 22942 5.1
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 3.3 3.36 85.2 0.35
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 3D2I 3.302 26.062 22903 1164 88.89 0.2576 0.2519 0.2571 0.3628 0.3645 RANDOM
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] -1.4951 -11.8301 -3.8657
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.273 f_angle_d 1.52 f_chiral_restr 0.091 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11098 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 176
Software Software Software Name Purpose HKL-2000 data collection CNS refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing