2B7U

Ribosome inactivating protein type 1 from Charybdis maritima AGG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6283100mM Mes, 16% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.24α = 90
b = 57.24β = 104.08
c = 51.088γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.649.63970.0640.06418.14.63561618.86
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6982.20.1860.1865.93.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTcombined model from PARTS OF 12 RIP's1.62033815178597.20.186480.1830.1820.208RANDOM18.21
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]
-0.74-0.420.370.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.882
r_dihedral_angle_4_deg23.992
r_dihedral_angle_3_deg15.362
r_dihedral_angle_1_deg5.496
r_scangle_it3.565
r_scbond_it2.446
r_mcangle_it1.669
r_angle_refined_deg1.598
r_mcbond_it1.123
r_angle_other_deg0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.882
r_dihedral_angle_4_deg23.992
r_dihedral_angle_3_deg15.362
r_dihedral_angle_1_deg5.496
r_scangle_it3.565
r_scbond_it2.446
r_mcangle_it1.669
r_angle_refined_deg1.598
r_mcbond_it1.123
r_angle_other_deg0.886
r_mcbond_other0.235
r_symmetry_vdw_other0.231
r_symmetry_vdw_refined0.23
r_nbd_refined0.22
r_nbd_other0.194
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.171
r_chiral_restr0.163
r_symmetry_hbond_refined0.085
r_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_metal_ion_other
r_sphericity_bonded
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2047
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms12

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling