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Crystal structure of the C-terminal 10 kDa subdomain from C. elegans Hsp70
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Preliminary model built using data from a mercury derivative crystal solved using MAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 55% ammonium sulphate, 0.5% PEG 400, 0.1M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.12 60.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.927 α = 90 b = 138.927 β = 90 c = 100.704 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2006-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.978 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.2 36 99.9 0.136 0.136 12.9 8.7 16809 16809 103.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 100 0.936 0.936 2 9.1 2399
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Preliminary model built using data from a mercury derivative crystal solved using MAD 3.2 36 16809 16232 820 96.694 0.269 0.2684 0.2819 0.2781 RANDOM 89.409
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] 1.749 1.749 -3.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.458 r_dihedral_angle_4_deg 33.938 r_dihedral_angle_3_deg 23.538 r_dihedral_angle_1_deg 8.172 r_angle_refined_deg 1.761 r_scangle_it 1.719 r_angle_other_deg 1.109 r_scbond_it 1.027 r_mcangle_it 0.815 r_scangle_other 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.458 r_dihedral_angle_4_deg 33.938 r_dihedral_angle_3_deg 23.538 r_dihedral_angle_1_deg 8.172 r_angle_refined_deg 1.761 r_scangle_it 1.719 r_angle_other_deg 1.109 r_scbond_it 1.027 r_mcangle_it 0.815 r_scangle_other 0.783 r_mcbond_it 0.5 r_mcangle_other 0.409 r_scbond_other 0.306 r_nbd_refined 0.296 r_xyhbond_nbd_refined 0.253 r_symmetry_vdw_other 0.25 r_symmetry_hbond_refined 0.23 r_xyhbond_nbd_other 0.223 r_nbtor_refined 0.216 r_nbd_other 0.204 r_chiral_restr 0.138 r_nbtor_other 0.1 r_mcbond_other 0.089 r_symmetry_vdw_refined 0.083 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3972 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing