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Crystal structure of the clp gene regulator ClgR from C. glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F51 PDB entry 3F51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.085 M HEPES, 8.5% PEG 8000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.08 α = 90 b = 55.08 β = 90 c = 129.61 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0685 SLS X10SA
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 1.75 42 100 0.057 24.56 10 20944 20938 1.7 3
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 1.75 1.85 100 0.799 2.56 8.5 3143
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB entry 3F51 1.75 41.96 3 1.7 19890 19890 1047 100 0.18449 0.18307 0.183 0.21254 0.2137 RANDOM 33.788
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] 0.82 0.82 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.77 r_dihedral_angle_4_deg 18.012 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 4.55 r_scangle_it 4.014 r_scbond_it 2.593 r_mcangle_it 1.578 r_angle_refined_deg 1.361 r_mcbond_it 0.873 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.77 r_dihedral_angle_4_deg 18.012 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 4.55 r_scangle_it 4.014 r_scbond_it 2.593 r_mcangle_it 1.578 r_angle_refined_deg 1.361 r_mcbond_it 0.873 r_nbtor_refined 0.296 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1132 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 30
Software Software Software Name Purpose gclient data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling