X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YG9PDB entries 1YG9, 1MLB
experimental modelPDB 1MLBPDB entries 1YG9, 1MLB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829820% PEG 10000, 0.1M Ammonium sulfate, 5mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.5164.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.004α = 90
b = 103.187β = 94.83
c = 146.329γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.85093.30.09811.13.351667-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.965.20.3012.2

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 entries 1YG9, 1MLB2.815049052261092.820.234780.232380.28058RANDOM14.999
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]
-0.39-0.47-1.331.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_3_deg16.615
r_dihedral_angle_4_deg14.651
r_dihedral_angle_1_deg6.442
r_angle_refined_deg1.048
r_nbtor_refined0.302
r_nbd_refined0.234
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.151
r_metal_ion_refined0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_3_deg16.615
r_dihedral_angle_4_deg14.651
r_dihedral_angle_1_deg6.442
r_angle_refined_deg1.048
r_nbtor_refined0.302
r_nbd_refined0.234
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.151
r_metal_ion_refined0.126
r_symmetry_hbond_refined0.125
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11600
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing