X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VKNPDB entry 1vkn

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529517% PEG 10000, 0.1 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6653.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.456α = 90
b = 78.214β = 127.46
c = 88.034γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.855091.36530859626
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9288.2

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 REPLACEMENTTHROUGHOUTPDB entry 1vkn1.85506222656669295691.070.163360.163360.16120.20498RANDOM14.308
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]
-0.38-0.260.64-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.704
r_dihedral_angle_4_deg17.861
r_dihedral_angle_3_deg12.606
r_dihedral_angle_1_deg5.847
r_scangle_it3.219
r_scbond_it2.004
r_angle_refined_deg1.495
r_mcangle_it1.298
r_mcbond_it0.782
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.704
r_dihedral_angle_4_deg17.861
r_dihedral_angle_3_deg12.606
r_dihedral_angle_1_deg5.847
r_scangle_it3.219
r_scbond_it2.004
r_angle_refined_deg1.495
r_mcangle_it1.298
r_mcbond_it0.782
r_nbtor_refined0.302
r_nbd_refined0.197
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.111
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5020
Nucleic Acid Atoms
Solvent Atoms688
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing