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N-terminal domain of Thiol:disulfide interchange protein DsbD in its reduced form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 28% PEG 4000, 0.1M ammonium sulphate, 0.1M sodium acetate pH 5.0, 10mM dithiothreitol , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.74 α = 90 b = 55.552 β = 90 c = 105.209 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2010-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 100 94.4 0.072 10.7 4.1 15011 14176 -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 1.8 1.86 72 0.366 2.3 1070
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-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 1L6P 1.8 31.13 13445 717 94.55 0.18632 0.18386 0.1816 0.23343 0.2294 RANDOM 22.921
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_4_deg 12.143 r_dihedral_angle_1_deg 6.448 r_scangle_it 5.52 r_scbond_it 3.396 r_mcangle_it 2.226 r_angle_refined_deg 1.899 r_mcbond_it 1.306 r_chiral_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.591 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_4_deg 12.143 r_dihedral_angle_1_deg 6.448 r_scangle_it 5.52 r_scbond_it 3.396 r_mcangle_it 2.226 r_angle_refined_deg 1.899 r_mcbond_it 1.306 r_chiral_restr 0.169 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction