3ZI8 | pdb_00003zi8

Structure of the R17A mutant of the Ralstonia soleanacerum lectin at 1.5 Angstrom in complex with L-fucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BT9PDB ENTRY 2BT9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530MM MGCL2, 30MM CACL2, 100MM MES/IMIDAZOLE PH 6.5, 12.5 % OF MPD, PEG1K AND PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.856.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.399α = 90
b = 72.399β = 90
c = 35.99γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.536.299.30.0515.95.4175232
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5898.70.314.85.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BT91.536.21662889299.010.13510.133570.150.16560.18RANDOM19.041
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]
0.330.330.33-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.774
r_sphericity_free19.038
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg6.849
r_sphericity_bonded6.48
r_rigid_bond_restr5.533
r_dihedral_angle_4_deg2.892
r_mcangle_it2.477
r_scbond_it2.22
r_mcbond_it2.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.774
r_sphericity_free19.038
r_dihedral_angle_3_deg12.848
r_dihedral_angle_1_deg6.849
r_sphericity_bonded6.48
r_rigid_bond_restr5.533
r_dihedral_angle_4_deg2.892
r_mcangle_it2.477
r_scbond_it2.22
r_mcbond_it2.198
r_mcbond_other2.16
r_angle_refined_deg1.614
r_angle_other_deg0.846
r_symmetry_vdw_refined0.257
r_nbd_refined0.241
r_symmetry_vdw_other0.207
r_nbd_other0.198
r_nbtor_refined0.192
r_xyhbond_nbd_refined0.165
r_chiral_restr0.114
r_nbtor_other0.093
r_symmetry_hbond_refined0.056
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 AtomsNumber
Protein Atoms682
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing