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Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a-b domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9WZK inactive mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.724 α = 90 b = 174.375 β = 103.08 c = 53.015 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 95 CCD ADSC QUANTUM 210r 2012-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.1 100 100 0.151 11.2 7.1 34783
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 2.1 2.18 100 0.69 3.3 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.1 32.281 34627 1742 99.965 0.193 0.1902 0.1982 0.2528 0.2598 RANDOM 28.138
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] -0.037 -0.084 0.063 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.556 r_dihedral_angle_6_deg 13.241 r_lrange_it 7.178 r_lrange_other 7.177 r_dihedral_angle_1_deg 6.691 r_dihedral_angle_2_deg 6.458 r_scangle_it 5.511 r_scangle_other 5.51 r_mcangle_it 3.912 r_mcangle_other 3.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.556 r_dihedral_angle_6_deg 13.241 r_lrange_it 7.178 r_lrange_other 7.177 r_dihedral_angle_1_deg 6.691 r_dihedral_angle_2_deg 6.458 r_scangle_it 5.511 r_scangle_other 5.51 r_mcangle_it 3.912 r_mcangle_other 3.912 r_scbond_it 3.49 r_scbond_other 3.489 r_mcbond_it 2.709 r_mcbond_other 2.708 r_angle_refined_deg 1.752 r_angle_other_deg 0.58 r_nbd_refined 0.219 r_nbd_other 0.202 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_other 0.104 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3918 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing