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Binding of kinetin in the active site of mistletoe lectin I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M2T PDB ENTRY 1M2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 2.5 293 1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, counter diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.59 73.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.573 α = 90 b = 107.573 β = 90 c = 310.633 γ = 120
Symmetry Space Group P 65 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 MAR CCD 165 mm 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8162 EMBL/DESY, HAMBURG X13
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 2.7 20 99.3 0.139 6.1 8.9 30058 30058
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 99 9.1
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 1M2T 2.7 19.97 28527 1517 99.14 0.17669 0.17409 0.1729 0.22586 0.2229 RANDOM 47.371
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] 1.52 0.76 1.52 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 21.651 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_1_deg 7.399 r_scangle_it 3.617 r_scbond_it 2.24 r_angle_refined_deg 2.049 r_mcangle_it 1.293 r_mcbond_it 0.668 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 21.651 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_1_deg 7.399 r_scangle_it 3.617 r_scbond_it 2.24 r_angle_refined_deg 2.049 r_mcangle_it 1.293 r_mcbond_it 0.668 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3922 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 181
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction