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Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMM PDB ENTRY 1PMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 290 PYRIDINE CHLORIDE, GLYCEROL,SODIUM CHLORIDE, SODIUM ACETATE, PEG 3000, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.58 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.1 α = 90 b = 117.1 β = 90 c = 196.4 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH 2002-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ELLIOTT GX-6 1.5418
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 2.05 29.27 95.6 0.091 9.97 60197 60197 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 91.1 0.26 4.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB ENTRY 1PMM 2.05 30 1 53367 53367 2857 89.34 0.151 0.151 0.14803 0.1479 0.19861 0.199 RANDOM 23.201
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] -0.89 -0.44 -0.89 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.94 r_scangle_it 4.33 r_scbond_it 2.64 r_mcangle_it 1.588 r_angle_refined_deg 1.446 r_mcbond_it 0.862 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.94 r_scangle_it 4.33 r_scbond_it 2.64 r_mcangle_it 1.588 r_angle_refined_deg 1.446 r_mcbond_it 0.862 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.1 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7107 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement