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X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MSA PDB ENTRY 1MSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 4M Sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.422 α = 90 b = 98.154 β = 90 c = 105.827 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MAR CCD 165 mm 2009-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 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 1.94 30 0.098 4.3 48106 3.84
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 1.94 2 0.33 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT PDB ENTRY 1MSA 1.94 30 30977 1647 85.52 0.18015 0.17773 0.22504 0.2358 RANDOM 25.909
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] 1.22 -1.42 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.795 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 18.649 r_dihedral_angle_1_deg 8.308 r_scangle_it 4.911 r_scbond_it 3.572 r_mcangle_it 2.306 r_angle_refined_deg 2.142 r_mcbond_it 1.382 r_chiral_restr 0.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.795 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 18.649 r_dihedral_angle_1_deg 8.308 r_scangle_it 4.911 r_scbond_it 3.572 r_mcangle_it 2.306 r_angle_refined_deg 2.142 r_mcbond_it 1.382 r_chiral_restr 0.264 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 3428 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SOLVE phasing REFMAC refinement SCALEPACK data scaling