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Crystal structure of yellow lupin LLPR-10.1A protein in complex with trans-zeatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 1.8 M (NH4)2SO4, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.97 α = 90 b = 63.91 β = 126.68 c = 47.56 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2005-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.38 99 99.2 0.054 24.74 4.1 34754 -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 1.38 1.43 99.6 0.209 6.48 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ICX 1.38 42.49 33857 896 99.19 0.14274 0.142 0.1532 0.17013 0.1743 RANDOM 16.105
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] -0.72 -1.12 -0.93 1.57
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.271 r_dihedral_angle_2_deg 31.231 r_sphericity_bonded 13.571 r_dihedral_angle_3_deg 9.76 r_dihedral_angle_1_deg 5.543 r_rigid_bond_restr 3.782 r_scbond_it 3.546 r_angle_refined_deg 1.987 r_dihedral_angle_4_deg 1.912 r_mcangle_it 1.633
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.271 r_dihedral_angle_2_deg 31.231 r_sphericity_bonded 13.571 r_dihedral_angle_3_deg 9.76 r_dihedral_angle_1_deg 5.543 r_rigid_bond_restr 3.782 r_scbond_it 3.546 r_angle_refined_deg 1.987 r_dihedral_angle_4_deg 1.912 r_mcangle_it 1.633 r_mcbond_it 1.415 r_mcbond_other 1.41 r_angle_other_deg 0.888 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 85
Software Software Software Name Purpose IS4CCDI data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling