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Crystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IFV PDB entry 1IFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.71 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.956 α = 90 b = 69.243 β = 90 c = 112.918 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MARRESEARCH mirrors 2000-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.9800 NSLS X9B
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 1.9 25 99.2 0.052 28.3 4.3 30830 30830 -3 30.8
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 1.9 1.97 97.8 0.412 2.7 3.2 3000
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 1IFV 1.9 20 28579 28579 1193 96.75 0.207 0.207 0.205 0.2129 0.251 0.2573 RANDOM 24.01
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 3.13 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.333 r_scangle_it 6.23 r_scbond_it 4.423 r_mcangle_it 3.013 r_angle_refined_deg 1.783 r_mcbond_it 1.779 r_angle_other_deg 0.926 r_symmetry_vdw_other 0.284 r_nbd_other 0.251 r_symmetry_hbond_refined 0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.333 r_scangle_it 6.23 r_scbond_it 4.423 r_mcangle_it 3.013 r_angle_refined_deg 1.783 r_mcbond_it 1.779 r_angle_other_deg 0.926 r_symmetry_vdw_other 0.284 r_nbd_other 0.251 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.105 r_metal_ion_refined 0.096 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing