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Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Cytokinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of LlPR-10.2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 1.2 M sodium citrate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.822 α = 90 b = 73.822 β = 90 c = 67.212 γ = 120
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 mirrors 2005-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8030 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 1.35 15 100 0.042 56.7 9.7 45685 45644 -1
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 1.35 1.4 100 0.67 2.5 10.1
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 (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 LlPR-10.2F 1.35 15 45685 44481 1163 99.99 0.14843 0.14725 0.1517 0.19438 0.2011 RANDOM 19.218
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] -0.37 -0.18 -0.37 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.155 r_sphericity_free 24.169 r_scangle_it 11.702 r_dihedral_angle_3_deg 11.498 r_sphericity_bonded 11.39 r_scbond_it 9.167 r_mcangle_it 6.031 r_dihedral_angle_1_deg 5.844 r_mcbond_it 5.053 r_rigid_bond_restr 4.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.155 r_sphericity_free 24.169 r_scangle_it 11.702 r_dihedral_angle_3_deg 11.498 r_sphericity_bonded 11.39 r_scbond_it 9.167 r_mcangle_it 6.031 r_dihedral_angle_1_deg 5.844 r_mcbond_it 5.053 r_rigid_bond_restr 4.477 r_mcbond_other 3.893 r_angle_refined_deg 2.043 r_angle_other_deg 0.96 r_dihedral_angle_4_deg 0.408 r_nbd_refined 0.215 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.19 r_metal_ion_refined 0.152 r_symmetry_vdw_other 0.151 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.112 r_symmetry_vdw_refined 0.102 r_nbtor_other 0.089 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1184 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing