4RZJ

Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with N-acetylglucosamine at 1.98 Angstrom resolution using crystals grown in different conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QGJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8298100mM sodium phosphate, 14% PEG 6000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.148α = 90
b = 130.148β = 90
c = 39.693γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARMOSAIC 225 mm CCDmirrors2014-11-13MSINGLE 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
11.9865.081000.08829.133.7156751567540.8
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)
11.982.0185.40.6741.53.5740

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 REPLACEMENTTHROUGHOUT4QGJ1.9865.07156751487080189.770.171710.171710.168340.21877RANDOM50.294
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]
-1.78-0.89-1.785.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.417
r_dihedral_angle_4_deg18.921
r_dihedral_angle_3_deg15.164
r_long_range_B_refined9.47
r_long_range_B_other9.292
r_scangle_other7.162
r_dihedral_angle_1_deg5.777
r_mcangle_other5.155
r_mcangle_it5.153
r_scbond_it4.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.417
r_dihedral_angle_4_deg18.921
r_dihedral_angle_3_deg15.164
r_long_range_B_refined9.47
r_long_range_B_other9.292
r_scangle_other7.162
r_dihedral_angle_1_deg5.777
r_mcangle_other5.155
r_mcangle_it5.153
r_scbond_it4.886
r_scbond_other4.862
r_mcbond_it3.823
r_mcbond_other3.823
r_angle_refined_deg1.626
r_angle_other_deg0.843
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms41

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling