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Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 7.5)
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 7.5 18 % PEG 4000, 0.1 M BIS-TRIS PH 7.5, 0.2 M NAI
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.83 α = 90 b = 93.83 β = 90 c = 36.63 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 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 46.93 99.7 0.2 7.8 4.9 12748 -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 2.12 98.5 0.65 2.5 4.9
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 46.93 12109 638 100 0.22 0.217 0.2197 0.274 0.2625 RANDOM 13.97
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] -0.09 -0.04 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.471 r_dihedral_angle_3_deg 17.916 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_1_deg 5.356 r_scangle_it 3.335 r_scbond_it 2.143 r_angle_refined_deg 1.477 r_mcangle_it 1.359 r_angle_other_deg 0.887 r_mcbond_it 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.471 r_dihedral_angle_3_deg 17.916 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_1_deg 5.356 r_scangle_it 3.335 r_scbond_it 2.143 r_angle_refined_deg 1.477 r_mcangle_it 1.359 r_angle_other_deg 0.887 r_mcbond_it 0.816 r_symmetry_vdw_other 0.342 r_symmetry_vdw_refined 0.304 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.199 r_nbd_other 0.181 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.088 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 1095 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing