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Structure of PDI-related Chaperone, Wind mutant-Y55K
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 8.2 0.1M TRIS-HCL PH 8.2-8.8 25 MM MGCL2 10% PEG4000 5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.51 64.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.421 α = 90 b = 119.095 β = 100.53 c = 64.034 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 MARRESEARCH 2005-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.25 20 97.8 0.06 16.83 4.67 22938 2
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 2.25 2.34 91.3 0.27 3.51 2.62
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 2.25 20 22938 1220 99.9 0.226 0.223 0.2254 0.292 0.2937 THIN SHELLS 45.38
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] 0.7 2.28 -1.09 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_1_deg 9.15 r_scangle_it 8.949 r_scbond_it 6.449 r_mcangle_it 4.068 r_angle_refined_deg 2.73 r_mcbond_it 2.598 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_1_deg 9.15 r_scangle_it 8.949 r_scbond_it 6.449 r_mcangle_it 4.068 r_angle_refined_deg 2.73 r_mcbond_it 2.598 r_nbtor_refined 0.317 r_nbd_refined 0.258 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.183 r_bond_refined_d 0.033 r_gen_planes_refined 0.01 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 2649 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing