X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9277SITTING DROP VAPOUR DIFFUSION, PROTEIN (15MG/ML) IN 100MM NACL, 0.1MM EDTA, 1.0MM (R, S)-DOBUTAMINE, 0.9MG/ML CHS, 0.6% HEGA-10, 0.1M BICINE PH9, 25% PEG600 AT 4 DEGREES C, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
3.7867

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.1α = 90
b = 61.6β = 108.9
c = 101.4γ = 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
12.649.995.60.137.13.83095332
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)
12.62.7491.30.721.93.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VT42.695.9229388156594.620.227720.225710.26636RANDOM48.484
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]
1.360.690.52-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.427
r_dihedral_angle_3_deg18.03
r_dihedral_angle_4_deg15.532
r_scangle_it5.756
r_dihedral_angle_1_deg4.995
r_scbond_it3.569
r_mcangle_it2.783
r_mcbond_it1.455
r_angle_refined_deg1.385
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.427
r_dihedral_angle_3_deg18.03
r_dihedral_angle_4_deg15.532
r_scangle_it5.756
r_dihedral_angle_1_deg4.995
r_scbond_it3.569
r_mcangle_it2.783
r_mcbond_it1.455
r_angle_refined_deg1.385
r_chiral_restr0.091
r_bond_refined_d0.011
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 Atoms4639
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms373

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing