4L66

Crystal structure of Ribosome inactivating protein from Momordica balsamina with highly ordered water structure in the substrate binding site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.729814% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.037α = 90
b = 130.037β = 90
c = 40.014γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2013-05-01MSINGLE 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
11.75099.90.06736.92782627826
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)
11.71.731000.3912.7

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 REPLACEMENTTHROUGHOUT3S9Q1.732.532642326423140199.820.155090.153070.19424RANDOM28.875
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]
-0.69-0.69-0.692.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.674
r_dihedral_angle_4_deg18.364
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg5.993
r_angle_refined_deg2.163
r_angle_other_deg0.969
r_chiral_restr0.132
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.674
r_dihedral_angle_4_deg18.364
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg5.993
r_angle_refined_deg2.163
r_angle_other_deg0.969
r_chiral_restr0.132
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms26

Software

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