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Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 5.0)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RJ1 PDB ENTRY 1RJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 19% PEG 4000, 0.1 M NAOAC PH 5.0, 0.2 M LI2SO4
Crystal Properties Matthews coefficient Solvent content 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.84 α = 90 b = 131.84 β = 90 c = 47.59 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC CCD 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.84 43.94 97.1 0.12 15.4 10.1 21167 -3
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 1.84 1.95 83.1 0.65 3.1 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RJ1 1.84 43.94 20107 1059 100 0.182 0.18 0.218 0.2574 RANDOM 23.99
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] 0.42 0.21 0.42 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 14.435 r_dihedral_angle_3_deg 13.883 r_dihedral_angle_1_deg 4.714 r_scangle_it 4.1 r_scbond_it 2.853 r_angle_refined_deg 1.42 r_mcangle_it 1.31 r_mcbond_it 1.206 r_angle_other_deg 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.693 r_dihedral_angle_4_deg 14.435 r_dihedral_angle_3_deg 13.883 r_dihedral_angle_1_deg 4.714 r_scangle_it 4.1 r_scbond_it 2.853 r_angle_refined_deg 1.42 r_mcangle_it 1.31 r_mcbond_it 1.206 r_angle_other_deg 0.87 r_symmetry_vdw_refined 0.408 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.181 r_nbtor_refined 0.173 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_other 0.151 r_nbtor_other 0.085 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing