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Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 9.5)
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 9.5 18 % PEG 4000, 0.1 M TRICINE PH 9.5, 0.2 M NAI
Crystal Properties Matthews coefficient Solvent content 2.1 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.05 α = 90 b = 50.22 β = 90 c = 131.38 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 CCD MARRESEARCH 2003-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 2.38 19.21 100 0.12 13.6 7.1 11192 -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 2.38 2.58 99.7 0.45 4.4 7.2
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 1RJ1 2.38 19.21 10602 558 100 0.202 0.198 0.2041 0.273 0.2792 RANDOM 37.44
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] -0.17 1.33 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.058 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 16.784 r_dihedral_angle_1_deg 7.015 r_scangle_it 2.611 r_scbond_it 1.707 r_angle_refined_deg 1.542 r_mcangle_it 1.065 r_angle_other_deg 0.917 r_mcbond_it 0.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.058 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 16.784 r_dihedral_angle_1_deg 7.015 r_scangle_it 2.611 r_scbond_it 1.707 r_angle_refined_deg 1.542 r_mcangle_it 1.065 r_angle_other_deg 0.917 r_mcbond_it 0.627 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.245 r_xyhbond_nbd_refined 0.23 r_symmetry_vdw_other 0.204 r_nbd_other 0.18 r_nbtor_refined 0.168 r_symmetry_vdw_refined 0.152 r_mcbond_other 0.133 r_nbtor_other 0.091 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 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_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 2134 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing