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ClpB NBD2 from T. thermophilus in complex with AMPPCP
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 7 293 0.2M sodium citrate, 0.1M HEPES/NaOH, 20% isopropanol, 2mM AMPPCP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.05 α = 90 b = 74.05 β = 90 c = 118.67 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 90 CCD MAR CCD 165 mm 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97926 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 1.9 25 99.9 0.074 14.1 28958 28959 -3 -3
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 1.9 2 100 0.554 3.8 3.8 4115
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 1.9 10 27262 27262 1447 99.73 0.21923 0.21923 0.21702 0.2319 0.26236 0.2733 RANDOM 34.589
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.832 r_angle_refined_deg 1.227 r_scbond_it 1.153 r_angle_other_deg 0.857 r_mcangle_it 0.572 r_mcbond_it 0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 5.34 r_scangle_it 1.832 r_angle_refined_deg 1.227 r_scbond_it 1.153 r_angle_other_deg 0.857 r_mcangle_it 0.572 r_mcbond_it 0.518 r_symmetry_vdw_other 0.211 r_symmetry_hbond_refined 0.193 r_nbd_refined 0.185 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.159 r_nbd_other 0.143 r_nbtor_other 0.08 r_mcbond_other 0.076 r_symmetry_vdw_refined 0.066 r_chiral_restr 0.065 r_xyhbond_nbd_other 0.017 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2557 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 36
Software Software Software Name Purpose MAR345 data collection CNS refinement REFMAC refinement XDS data reduction XSCALE data scaling CNS phasing