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X-ray structure of ComE D58A REC domain from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B1N PDB entry 4B1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.2 25% PEG 3350, 0.2M Sodium formate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.47 α = 90 b = 91.47 β = 90 c = 134.84 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 100 PIXEL PSI PILATUS 6M 2013-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
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 3.15 45.7 99.67 0.144 0.144 15 9.22 11136 11099 3.16 3.16 65.55
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) 1 3.15 3.46 99.7 0.144 0.144 15 9.2 11099
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 4B1N 3.15 45.7 2 1.99 11136 11086 553 99.58 0.2745 0.272 0.2695 0.322 0.3153 4.99%
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] -24.3346 -24.3346 48.6691
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.802 f_angle_d 0.878 f_chiral_restr 0.061 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4333 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose APEX data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling