3NJS

Crystal structure of the complex formed between typeI ribosome inactivating protein and lactose at 2.1A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AHA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3247.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.44α = 90
b = 130.44β = 90
c = 38.473γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2010-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.165.299.10.0726133901339035.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1495.10.4331.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AHA2.137.65133901339070699.120.226310.225640.223820.26073RANDOM54.385
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]
-4.21-2.1-4.216.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.631
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg14.921
r_scangle_it2.606
r_dihedral_angle_1_deg1.654
r_angle_refined_deg1.627
r_scbond_it1.61
r_mcangle_it1.59
r_mcbond_it0.886
r_symmetry_vdw_refined0.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.631
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg14.921
r_scangle_it2.606
r_dihedral_angle_1_deg1.654
r_angle_refined_deg1.627
r_scbond_it1.61
r_mcangle_it1.59
r_mcbond_it0.886
r_symmetry_vdw_refined0.363
r_nbtor_refined0.334
r_symmetry_hbond_refined0.306
r_nbd_refined0.257
r_xyhbond_nbd_refined0.181
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms57

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling