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Crystal structure of 2-methylisocitrate lyase (PrpB) from Salmonella enterica serovar typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 Imidazole,Sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K 2 VAPOR DIFFUSION, HANGING DROP 8 291 Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K 3 VAPOR DIFFUSION, SITTING DROP 8 291 Sodium chloride, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K 4 VAPOR DIFFUSION, SITTING DROP 4.5 277 Sodium formate, Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.812 α = 90 b = 99.086 β = 90 c = 201.571 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 IMAGE PLATE MARRESEARCH Osmic mirrors 2003-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 100 92.9 0.061 0.061 15.5 5.5 74393 69022 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.17 97 0.421 0.423 5.2 5.8 7079
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-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 1MUM 2.1 19.99 69022 3514 92.9 0.205 0.205 0.2042 0.232 0.232 RANDOM 38.8
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] -5.42 6.09 -0.68
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scangle_it 3.16 c_mcangle_it 2.23 c_scbond_it 2.17 c_mcbond_it 1.44 c_angle_deg 1.1 c_improper_angle_d 0.86 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8220 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing