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Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QIM PDB entry 2QIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 1.4 M Sodium citrate, 0.1 M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.86 33.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.362 α = 90 b = 73.256 β = 90 c = 99.956 γ = 90
Symmetry Space Group C 2 2 21
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 MAR CCD 165 mm mirrors 2005-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 EMBL/DESY, HAMBURG X11
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 1.95 40 99.56 0.075 20.8 5.7 9529 -3 37.9
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 1.95 2.02 96.8 0.398 3.8 5.4
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 2QIM 1.95 15 8631 860 99.54 0.19323 0.18788 0.1942 0.2465 0.2421 RANDOM 30.611
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] -1.66 -1.34 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_3_deg 16.875 r_scangle_it 6.456 r_dihedral_angle_1_deg 6.214 r_dihedral_angle_4_deg 5.89 r_scbond_it 4.229 r_angle_refined_deg 1.878 r_mcangle_it 1.85 r_mcbond_it 1.044 r_angle_other_deg 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_3_deg 16.875 r_scangle_it 6.456 r_dihedral_angle_1_deg 6.214 r_dihedral_angle_4_deg 5.89 r_scbond_it 4.229 r_angle_refined_deg 1.878 r_mcangle_it 1.85 r_mcbond_it 1.044 r_angle_other_deg 0.941 r_nbd_refined 0.244 r_mcbond_other 0.241 r_symmetry_hbond_refined 0.217 r_nbd_other 0.211 r_nbtor_refined 0.195 r_metal_ion_refined 0.192 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.152 r_symmetry_vdw_other 0.144 r_chiral_restr 0.106 r_nbtor_other 0.096 r_bond_refined_d 0.018 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 1155 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing