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Crystal structure of Protein L-isoaspartyl methyltransferase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 Hepes-Na, monosodium dihydrogen phosphate, monopotassium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.92 35.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.3 α = 74 b = 55.06 β = 74.7 c = 67.49 γ = 85.57
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2009-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.00
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 1.8 25 96.2 0.056 10.7 2.8 62259
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 1.8 1.9 95 0.207 3.9 2.8 8977
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 2YXE 1.8 25 59103 3156 96.21 0.2151 0.2134 0.2179 0.2472 0.2508 RANDOM 42.2995
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] 0.49 0.02 -0.24 1.83 -2.91 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.852 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 15.175 r_dihedral_angle_1_deg 5.474 r_scangle_it 3.512 r_scbond_it 2.165 r_mcangle_it 1.848 r_angle_refined_deg 1.24 r_mcbond_it 1.066 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.852 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 15.175 r_dihedral_angle_1_deg 5.474 r_scangle_it 3.512 r_scbond_it 2.165 r_mcangle_it 1.848 r_angle_refined_deg 1.24 r_mcbond_it 1.066 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6117 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 140
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction