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Crystal structure of rice protein disulfide isomerase-like protein OsPDIL2-3 a0 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9WZL domain a of the same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2M ammonium sulfate, 0.2M lithium sulfate, 0.2M diammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.94 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.773 α = 90 b = 61.773 β = 90 c = 100.761 γ = 90
Symmetry Space Group P 41 21 2
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 315r 2012-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 98 0.049 48.8 23.8 11788
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 97.5 0.702 5.1 24.5
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 30.906 11708 608 97.803 0.196 0.1944 0.2044 0.2221 0.2377 RANDOM 53.576
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] 1.881 1.881 -3.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.329 r_dihedral_angle_6_deg 14.215 r_lrange_other 12.683 r_lrange_it 12.668 r_scangle_it 10.379 r_scangle_other 10.372 r_dihedral_angle_2_deg 7.459 r_mcangle_it 6.788 r_mcangle_other 6.785 r_scbond_it 6.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.329 r_dihedral_angle_6_deg 14.215 r_lrange_other 12.683 r_lrange_it 12.668 r_scangle_it 10.379 r_scangle_other 10.372 r_dihedral_angle_2_deg 7.459 r_mcangle_it 6.788 r_mcangle_other 6.785 r_scbond_it 6.741 r_scbond_other 6.734 r_dihedral_angle_1_deg 6.45 r_mcbond_it 4.906 r_mcbond_other 4.835 r_angle_refined_deg 1.61 r_angle_other_deg 0.541 r_nbd_refined 0.228 r_nbd_other 0.206 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.145 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.079 r_bond_refined_d 0.007 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 917 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing