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Crystal structure of the Parkia platycephala seed lectin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 4000, isopropanol, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.597 α = 90 b = 68.511 β = 90 c = 208.531 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 2002-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.9300 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2 104 100 0.059 0.055 9.5 4.9 31543 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.002 2.11 65.1 0.101 0.101 4.4 1.4 2060
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.5 30 2 2 29482 27927 1555 95.75 0.21496 0.21525 0.2138 0.211 0.24297 0.2422 RANDOM 32.576
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] 0.24 -0.34 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.551 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 17.587 r_dihedral_angle_1_deg 7.703 r_scangle_it 3.374 r_scbond_it 2.076 r_mcangle_it 1.756 r_angle_refined_deg 1.711 r_mcbond_it 0.996 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.551 r_dihedral_angle_4_deg 19.215 r_dihedral_angle_3_deg 17.587 r_dihedral_angle_1_deg 7.703 r_scangle_it 3.374 r_scbond_it 2.076 r_mcangle_it 1.756 r_angle_refined_deg 1.711 r_mcbond_it 0.996 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.226 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6650 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing