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Crystal structure of the protein-disulfide isomerase related chaperone ERp29
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 VAPOR DIFFUSION, HANGING DROP 277 10 mg/ml protein in 5 mM HEPES, pH 7.5, 25 mM NaCl, 0.0025% (v/v) beta-mercaptoethanol was equlibrated with a reservoir containing 0.45 M (NH4)2SO4, 0.1 M sodium acetate buffer, pH 4.5 and 18-20% (w/v) PEG 2000 monomethyl ether. Crystals of about 0.1 mm in size grew in two days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.044 α = 90 b = 68.025 β = 107.46 c = 70.088 γ = 90
Symmetry Space Group P 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 180 CCD MAR CCD 130 mm 2003-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.96676 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.9 28.981 94.6 0.075 0.075 7.3 5.8 11070 89.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.599 0.599 1.3 5.9 1712
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 1OVN 2.9 28.98 11701 11068 560 94.69 0.265 0.265 0.265 0.2597 0.279 0.2581 RANDOM 54.235
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] 0.11 7.49 -3.12 7.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.033 r_dihedral_angle_3_deg 19.726 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_1_deg 5.066 r_angle_refined_deg 1.597 r_mcangle_it 1.272 r_scangle_it 1.083 r_mcbond_it 0.771 r_scbond_it 0.684 r_symmetry_vdw_refined 0.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.033 r_dihedral_angle_3_deg 19.726 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_1_deg 5.066 r_angle_refined_deg 1.597 r_mcangle_it 1.272 r_scangle_it 1.083 r_mcbond_it 0.771 r_scbond_it 0.684 r_symmetry_vdw_refined 0.391 r_nbtor_refined 0.361 r_nbd_refined 0.346 r_symmetry_hbond_refined 0.332 r_xyhbond_nbd_refined 0.293 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3526 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction