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Peptide-binding domain of Heat shock 70 kDa protein D precursor from C.elegans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUW PDB entry 1YUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 1.4 M Tri-sodium citrate, 0.1 M HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.172 α = 90 b = 26.688 β = 115.14 c = 60.995 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 SBC-3 2006-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97970 APS 19-BM
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 1.85 30.44 91.6 0.072 15.1 3.2 12530 12530 28.6
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 1.85 1.92 55.2 0.334 1.97 2.2 754
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 PDB entry 1YUW 1.85 30.44 11283 11283 1237 91.2 0.1735 0.1735 0.1689 0.1684 0.2124 0.2112 RANDOM 23.253
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] 0.51 -0.29 -0.85 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 15.504 r_dihedral_angle_1_deg 6.278 r_scangle_it 3.745 r_scbond_it 2.322 r_angle_refined_deg 1.555 r_mcangle_it 1.335 r_mcbond_it 0.895 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 15.504 r_dihedral_angle_1_deg 6.278 r_scangle_it 3.745 r_scbond_it 2.322 r_angle_refined_deg 1.555 r_mcangle_it 1.335 r_mcbond_it 0.895 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1145 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing