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Crystal structure of the C-terminal domain of E. coli KefC in complex with KefF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QR2 PDB entries 2QR2, 1LSS experimental model PDB 1LSS PDB entries 2QR2, 1LSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 12% MPD, 10% PEG 3350, 60mM MgCl2, 100mM HEPES pH 7.0, 1mM NAD+, 1mM HALESDIE peptide, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.47 α = 90 b = 85.015 β = 90 c = 188.702 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 CCD ADSC QUANTUM 315 2007-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0000 SSRL BL7-1
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 2.4 50 99.7 0.091 18.4 39348 39230
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 2.4 2.49 100 0.391 5.7
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 PDB entries 2QR2, 1LSS 2.4 50 39230 2074 99.45 0.19951 0.19741 0.1962 0.23861 0.2365 RANDOM 29.374
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] -0.15 0.93 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.597 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_1_deg 6.62 r_scangle_it 3.568 r_scbond_it 2.39 r_mcangle_it 1.496 r_angle_refined_deg 1.407 r_mcbond_it 1.262 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.597 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_1_deg 6.62 r_scangle_it 3.568 r_scbond_it 2.39 r_mcangle_it 1.496 r_angle_refined_deg 1.407 r_mcbond_it 1.262 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5531 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 111
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling