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ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Tris/HCl, 15% isopropanol, 10mM magnesium chloride, 2mM AMPPCP, 100mM guanidinium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.8 α = 90 b = 74.8 β = 90 c = 119.5 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 2013-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9120 SLS X10SA
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 44 100 0.043 29.1 10.3 25581 25581 -3 -3 41.1
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 2.1 100 0.821 3 10.6 3479
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 4LJ5 2 43.92 24325 24325 1256 100 0.21935 0.21935 0.2172 0.2228 0.26343 0.2726 RANDOM 46.841
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] 0.3 0.15 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.567 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_1_deg 5.09 r_scangle_it 2.766 r_scbond_it 1.613 r_angle_refined_deg 1.256 r_mcangle_it 0.924 r_mcbond_it 0.489 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.567 r_dihedral_angle_4_deg 15.694 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_1_deg 5.09 r_scangle_it 2.766 r_scbond_it 1.613 r_angle_refined_deg 1.256 r_mcangle_it 0.924 r_mcbond_it 0.489 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 36
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling