3MVG

Native structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M2TPDB ENTRY 1M2T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52931.9M ammonium sulfate in 20% w/v glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.879α = 90
b = 84.809β = 97.67
c = 69.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.81480EMBL/DESY, HAMBURGX11

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
11.253099.80.0510.44725.64.41575962.617.62
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)
11.2471.28980.6490.452.674.47666

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1M2T1.2530157596789399.60.169310.168460.18542RANDOM17.883
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]
0.280.71-0.110.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.805
r_dihedral_angle_4_deg17.331
r_dihedral_angle_3_deg11.455
r_dihedral_angle_1_deg5.7
r_scangle_it2.307
r_scbond_it1.47
r_angle_refined_deg1.185
r_mcangle_it0.987
r_mcbond_it0.52
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.805
r_dihedral_angle_4_deg17.331
r_dihedral_angle_3_deg11.455
r_dihedral_angle_1_deg5.7
r_scangle_it2.307
r_scbond_it1.47
r_angle_refined_deg1.185
r_mcangle_it0.987
r_mcbond_it0.52
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3990
Nucleic Acid Atoms
Solvent Atoms756
Heterogen Atoms109

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling