4ZT8

Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a pyrimidine base, cytosine at 1.98 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S9Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG 6000, 0.1M Sodium Phosphate
Crystal Properties
Matthews coefficientSolvent content
2.4148.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.258α = 90
b = 130.258β = 90
c = 39.939γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2013-05-01MSINGLE 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
11.9837.6399.90.07332.34.21667116671
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)
11.982.0199.80.2834.2

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 REPLACEMENTTHROUGHOUT3S9Q1.9837.631667189099.850.179590.177660.20423RANDOM30.105
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]
-0.69-0.69-0.692.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.219
r_dihedral_angle_4_deg19.434
r_dihedral_angle_3_deg13.153
r_dihedral_angle_1_deg5.046
r_long_range_B_refined4.501
r_long_range_B_other4.183
r_scangle_other1.983
r_mcangle_it1.844
r_mcangle_other1.844
r_scbond_it1.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.219
r_dihedral_angle_4_deg19.434
r_dihedral_angle_3_deg13.153
r_dihedral_angle_1_deg5.046
r_long_range_B_refined4.501
r_long_range_B_other4.183
r_scangle_other1.983
r_mcangle_it1.844
r_mcangle_other1.844
r_scbond_it1.148
r_scbond_other1.147
r_angle_refined_deg1.089
r_mcbond_it1.071
r_mcbond_other1.07
r_angle_other_deg0.72
r_chiral_restr0.057
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building