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Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpC1 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M SODIUM CITRATE DEHYDRATE, 1.0M AMMONIUM PHOSPHATE MONOBASIC
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.1 α = 90 b = 44.29 β = 90 c = 97.56 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 103 CCD MARMOSAIC 225 mm CCD 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9794 RRCAT INDUS-2 PX-BL21
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 1.2 17.54 97.9 0.067 9.4 4.8 54126 11.9
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 1.2 1.26 98.4 0.565 2.5 4.7
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WDC 1.2 17.54 51310 2742 97.9 0.147 0.167 0.1828 RANDOM 18
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] -1.84 0.5 1.34
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.721 r_dihedral_angle_2_deg 29.94 r_dihedral_angle_4_deg 17.249 r_sphericity_bonded 16.688 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 5.202 r_long_range_B_refined 4.138 r_long_range_B_other 3.934 r_scangle_other 3.885 r_scbond_other 3.262
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.721 r_dihedral_angle_2_deg 29.94 r_dihedral_angle_4_deg 17.249 r_sphericity_bonded 16.688 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 5.202 r_long_range_B_refined 4.138 r_long_range_B_other 3.934 r_scangle_other 3.885 r_scbond_other 3.262 r_scbond_it 3.226 r_rigid_bond_restr 3.074 r_mcangle_other 2.64 r_mcangle_it 2.636 r_mcbond_it 2.158 r_mcbond_other 2.144 r_angle_refined_deg 1.931 r_angle_other_deg 1.035 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1141 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 25
Software Software Software Name Purpose Aimless data reduction Aimless data scaling MOLREP phasing REFMAC refinement