X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKUPDB entry 1DKU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.928920% PEG 3350, 0.2M Magnesium formate, pH 5.9, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.346.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.966α = 90
b = 123.242β = 90
c = 197.364γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS2008-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.00000APS23-ID-D

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
12.350980.097.9641722
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)
12.32.3887.10.494.43648

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 1DKU2.346.9341695211097.870.2080.2060.255RANDOM48.513
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]
0.7-1.110.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.727
r_dihedral_angle_4_deg18.849
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg6.432
r_scangle_it2.1
r_angle_refined_deg1.324
r_scbond_it1.254
r_mcangle_it0.894
r_mcbond_it0.519
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.727
r_dihedral_angle_4_deg18.849
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg6.432
r_scangle_it2.1
r_angle_refined_deg1.324
r_scbond_it1.254
r_mcangle_it0.894
r_mcbond_it0.519
r_nbtor_refined0.299
r_nbd_refined0.197
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.141
r_chiral_restr0.09
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6637
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms104

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection