4M5A

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina inhibited by asymmetric dimethyl arginine at 1.70 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829814% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.257α = 90
b = 130.257β = 90
c = 39.74γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2013-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7501000.069232610126101
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)
11.71.7999.90.5965

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3S9Q1.737.512610126101138499.390.208080.208080.201460.24084RANDOM28.212
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]
-0.55-0.55-0.551.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg16.656
r_dihedral_angle_3_deg14.941
r_dihedral_angle_1_deg5.366
r_long_range_B_refined4.997
r_long_range_B_other4.749
r_scangle_other1.982
r_mcangle_it1.897
r_mcangle_other1.897
r_angle_refined_deg1.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg16.656
r_dihedral_angle_3_deg14.941
r_dihedral_angle_1_deg5.366
r_long_range_B_refined4.997
r_long_range_B_other4.749
r_scangle_other1.982
r_mcangle_it1.897
r_mcangle_other1.897
r_angle_refined_deg1.211
r_scbond_it1.154
r_scbond_other1.153
r_mcbond_other1.07
r_mcbond_it1.069
r_angle_other_deg0.813
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms28

Software

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