3Q4P

Crystal structure of the complex of type I ribosome inactivating protein with 7n-methyl -8-hydroguanosine-5-p-diphosphate at 1.8 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRWPDB ENTRY 3MRW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.848α = 90
b = 129.848β = 90
c = 39.717γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2010-10-21MSINGLE 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
11.837.593.20.04233.32151124.6
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)
11.81.8362.30.272.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3MRW1.837.452151120408109893.180.183030.180840.22597RANDOM32.621
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]
-0.33-0.16-0.330.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.928
r_dihedral_angle_4_deg15.897
r_dihedral_angle_3_deg12.999
r_dihedral_angle_1_deg5.422
r_scangle_it3.814
r_scbond_it2.722
r_angle_refined_deg1.72
r_mcangle_it1.605
r_mcbond_it1.05
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.928
r_dihedral_angle_4_deg15.897
r_dihedral_angle_3_deg12.999
r_dihedral_angle_1_deg5.422
r_scangle_it3.814
r_scbond_it2.722
r_angle_refined_deg1.72
r_mcangle_it1.605
r_mcbond_it1.05
r_nbtor_refined0.314
r_nbd_refined0.212
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.126
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms56

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling