4GUW

Crystal structure of type 1 Ribosome inactivating protein from Momordica balsamina with lipopolysaccharide at 1.6 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.235α = 90
b = 130.235β = 90
c = 39.82γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2012-05-22MSINGLE 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
11.665.1299.70.03838.833138
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)
11.61.630.5191.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3MRY1.665.1131467168199.710.192890.191270.22267RANDOM29.864
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]
-1.12-0.56-1.121.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.314
r_dihedral_angle_4_deg23.65
r_dihedral_angle_3_deg14.268
r_scangle_it6.067
r_dihedral_angle_1_deg5.668
r_scbond_it3.982
r_angle_refined_deg2.804
r_mcangle_it2.52
r_mcbond_it1.59
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.314
r_dihedral_angle_4_deg23.65
r_dihedral_angle_3_deg14.268
r_scangle_it6.067
r_dihedral_angle_1_deg5.668
r_scbond_it3.982
r_angle_refined_deg2.804
r_mcangle_it2.52
r_mcbond_it1.59
r_chiral_restr0.148
r_bond_refined_d0.031
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms83

Software

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