X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VT4PDB ENTRY 2VT4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5277SITTING DROP VAPOUR DIFFUSION, PROTEIN (14.5MG/ML) IN 100MM NACL, 0.1MM EDTA, 1.0MM (R, S)-DOBUTAMINE, 1.3MG/ML CHS, 0.55% HEGA-10, 0.1M TRIS-HCL PH8.5, 25% PEG600 AT 4 DEGREES C
Crystal Properties
Matthews coefficientSolvent content
3.7867

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90α = 90
b = 60.5β = 110.2
c = 101.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.544.793.80.156.22.93366546.6
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)
12.52.6482.80.511.92.6

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 2VT42.595.6531994167193.670.227920.226460.25551RANDOM36.983
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]
0.691.252.07-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.699
r_dihedral_angle_4_deg19.024
r_dihedral_angle_3_deg17.741
r_scangle_it6.478
r_dihedral_angle_1_deg5.195
r_scbond_it4.05
r_mcangle_it3.233
r_mcbond_it1.714
r_angle_refined_deg1.473
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.699
r_dihedral_angle_4_deg19.024
r_dihedral_angle_3_deg17.741
r_scangle_it6.478
r_dihedral_angle_1_deg5.195
r_scbond_it4.05
r_mcangle_it3.233
r_mcbond_it1.714
r_angle_refined_deg1.473
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4640
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms374

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing