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Structure of PDI-related Chaperone, Wind mutant-Y53S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OVN PDB ENTRY 1OVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 PROTEIN: 10.0MG/ML Y53S IN 5MM HEPES PH7.5, 25MM NACL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH6.0, 50MM NACL, 18%(V/V) PEG 400 5% GLYCEROL CRYO: 0.1M MES PH6.0, 25%(V/V) PEG 400, 10%(V/V)GLYCEROL,50MM NACL, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.476 α = 90 b = 50.557 β = 112.06 c = 98.9 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MARRESEARCH 2003-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 1.75 25 99.1 0.04 19.32 3.86 47523 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 1.75 1.85 95.9 0.26 3.96 3
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 PDB ENTRY 1OVN 1.75 25 47523 2487 100 0.222 0.219 0.2164 0.268 0.2595 RANDOM 26.53
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] 0.34 -0.55 -0.47 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.054 r_dihedral_angle_4_deg 14.404 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 5.47 r_scangle_it 4.464 r_scbond_it 3.002 r_angle_refined_deg 1.784 r_mcangle_it 1.752 r_mcbond_it 1.04 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.054 r_dihedral_angle_4_deg 14.404 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 5.47 r_scangle_it 4.464 r_scbond_it 3.002 r_angle_refined_deg 1.784 r_mcangle_it 1.752 r_mcbond_it 1.04 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.134 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3299 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing