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DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 5 mM erythrose 4-phosphate, 5 mM phosphoenolpyruvate, 30% (w/v) D-(+)-galactose
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.193 α = 90 b = 52.908 β = 115.711 c = 150.481 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 6M 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 64.45 96.1 0.078 0.091 0.047 0.997 12.8 3.7 66903 1.35 23.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.9 0.391 0.461 0.241 0.883 3.2 3.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CKS 2.3 49.65 1.35 66766 1991 99.69 0.1953 0.1943 0.1937 0.2276 0.2265 28.15
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 15.2437 f_angle_d 1.3513 f_chiral_restr 0.0714 f_bond_d 0.0123 f_plane_restr 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10228 Nucleic Acid Atoms Solvent Atoms 925 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing