7VUB

Phloem lectin (PP2) complex with Nitrobenzene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VS6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2951.0 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.81α = 90
b = 70.47β = 90
c = 101.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.250.971000.07312.526.6258587811.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.221.270.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7VS61.250.997099476599.9710.1620.16030.189316.129
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]
-2.6761.7560.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_rigid_bond_restr29.728
r_dihedral_angle_4_deg17.029
r_dihedral_angle_3_deg10.032
r_dihedral_angle_1_deg7.225
r_scbond_other5.01
r_scbond_it5.008
r_scangle_it4.338
r_scangle_other4.336
r_lrange_it3.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_rigid_bond_restr29.728
r_dihedral_angle_4_deg17.029
r_dihedral_angle_3_deg10.032
r_dihedral_angle_1_deg7.225
r_scbond_other5.01
r_scbond_it5.008
r_scangle_it4.338
r_scangle_other4.336
r_lrange_it3.955
r_lrange_other3.914
r_mcangle_it3.036
r_mcangle_other3.035
r_mcbond_it2.844
r_mcbond_other2.841
r_angle_other_deg2.401
r_angle_refined_deg2.026
r_symmetry_nbd_other0.221
r_symmetry_xyhbond_nbd_refined0.197
r_nbd_refined0.185
r_nbtor_refined0.181
r_symmetry_nbd_refined0.17
r_nbd_other0.128
r_chiral_restr0.113
r_xyhbond_nbd_refined0.112
r_ncsr_local_group_10.093
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.044
r_gen_planes_other0.037
r_bond_other_d0.036
r_bond_refined_d0.018
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2413
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing