X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ABRAbrin-a (PDB code: 1ABR)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG 8000, TRIS-HCL BUFFER, PH 8.5, , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.4572.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.122α = 90
b = 141.122β = 90
c = 105.253γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARRESEARCH2005-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9A0.978NSLSX9A

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
13.529.3195.70.09513.13.81136021
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)
13.53.796.80.5392.33.8

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 REPLACEMENTTHROUGHOUTAbrin-a (PDB code: 1ABR)3.529.311024611151000.200790.194810.25547RANDOM51.741
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.285
r_dihedral_angle_3_deg22.527
r_dihedral_angle_4_deg19.125
r_dihedral_angle_1_deg9.471
r_angle_refined_deg1.725
r_scangle_it1.387
r_scbond_it0.798
r_mcangle_it0.523
r_nbtor_refined0.326
r_symmetry_vdw_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.285
r_dihedral_angle_3_deg22.527
r_dihedral_angle_4_deg19.125
r_dihedral_angle_1_deg9.471
r_angle_refined_deg1.725
r_scangle_it1.387
r_scbond_it0.798
r_mcangle_it0.523
r_nbtor_refined0.326
r_symmetry_vdw_refined0.31
r_mcbond_it0.282
r_symmetry_hbond_refined0.276
r_nbd_refined0.266
r_xyhbond_nbd_refined0.164
r_chiral_restr0.127
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3983
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms45

Software

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