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J-domain of dnj-12 from Caenorhabditis elegans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O37 2O37 PDB ENTRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.664 α = 90 b = 51.758 β = 90 c = 85.803 γ = 90
Symmetry Space Group I 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 100 CCD SBC-3 2006-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 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 34.5 99.9 0.052 34.8 6.5 7363 7363 38.7
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 1.9 99.9 0.601 3.04 6.8 604
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 2O37 PDB ENTRY 1.86 34.6 7358 7358 342 99.18 0.2204 0.2204 0.2191 0.2195 0.2472 0.2481 RANDOM 23.324
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] 1.11 -0.42 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.531 r_dihedral_angle_3_deg 17.731 r_dihedral_angle_4_deg 11.504 r_dihedral_angle_1_deg 5.437 r_scangle_it 3.901 r_scbond_it 2.616 r_mcangle_it 1.692 r_angle_refined_deg 1.566 r_mcbond_it 1.203 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.531 r_dihedral_angle_3_deg 17.731 r_dihedral_angle_4_deg 11.504 r_dihedral_angle_1_deg 5.437 r_scangle_it 3.901 r_scbond_it 2.616 r_mcangle_it 1.692 r_angle_refined_deg 1.566 r_mcbond_it 1.203 r_nbtor_refined 0.315 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 534 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing