5CST

Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine diphosphate at 1.78 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
2.4449.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.216α = 90
b = 130.216β = 90
c = 40.458γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2012-11-11MSINGLE 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
11.7838.1199.80.065344.12295822958
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8196.92.6

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 REPLACEMENTTHROUGHOUT3S9Q1.7838.1122958123899.030.155450.150570.18878RANDOM29.159
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]
-1.26-1.26-1.264.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.915
r_dihedral_angle_4_deg15.703
r_dihedral_angle_3_deg12.318
r_long_range_B_refined7.688
r_long_range_B_other7.688
r_dihedral_angle_1_deg6.037
r_scangle_other5.687
r_scbond_it3.927
r_scbond_other3.914
r_mcangle_other3.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.915
r_dihedral_angle_4_deg15.703
r_dihedral_angle_3_deg12.318
r_long_range_B_refined7.688
r_long_range_B_other7.688
r_dihedral_angle_1_deg6.037
r_scangle_other5.687
r_scbond_it3.927
r_scbond_other3.914
r_mcangle_other3.218
r_mcangle_it3.216
r_mcbond_it2.512
r_mcbond_other2.503
r_angle_refined_deg2.039
r_angle_other_deg0.958
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms246
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building