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GriE in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 MORPHEUS (Molecular Dimensions) condition F1:
0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 50 % v/v Precipitant Mix 1
co-crystallization with:
10 mM L-leucine, 10 mM alpha-ketoglutarate, 10 mM DTT, 125.5 mM Tris/HCl and 1 mM 1 mM MnCl2 and 2 mM Na-ascorbate.
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.74 α = 90 b = 56.061 β = 112.46 c = 73.802 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 2M-F 2013-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.529 68.727 94.2 0.093 0.038 0.995 11 6.7 80188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.529 1.555 99.5 0.867 0.362 0.757 2.1 6.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NCH 1.529 51.91 1.34 80165 4026 94.24 0.1563 0.1554 0.156 0.1734 0.1746 copied free R flags from substrate complex (5NCI)
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 15.075 f_angle_d 0.923 f_chiral_restr 0.057 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4080 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing