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ClpP1 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1 M Bis-Tris, 0.2 M Li2SO4, 17% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.95 α = 90 b = 109.06 β = 93.16 c = 196.26 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 50 99.7 0.062 16.2 3.4 399725 398526 2 2
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 2.1 99.8 0.58 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3V5E 2 15 378598 378598 19927 99.69 0.21 0.19283 0.19179 0.1917 0.21288 0.2129 RANDOM 35.119
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] 0.21 -0.33 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.999 r_sphericity_free 21.976 r_dihedral_angle_4_deg 16.396 r_dihedral_angle_3_deg 13.998 r_sphericity_bonded 11.624 r_dihedral_angle_1_deg 4.232 r_rigid_bond_restr 1.045 r_angle_refined_deg 0.913 r_chiral_restr 0.066 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.999 r_sphericity_free 21.976 r_dihedral_angle_4_deg 16.396 r_dihedral_angle_3_deg 13.998 r_sphericity_bonded 11.624 r_dihedral_angle_1_deg 4.232 r_rigid_bond_restr 1.045 r_angle_refined_deg 0.913 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37660 Nucleic Acid Atoms Solvent Atoms 2899 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling