X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H1EPDB ENTRIES 2H1E,1Z63,1Z3I
experimental modelPDB 1Z63PDB ENTRIES 2H1E,1Z63,1Z3I
experimental modelPDB 1Z3IPDB ENTRIES 2H1E,1Z63,1Z3I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729818% PEG 3350; 400 mM K+/Na+ tartrate; 5% xylitol; 10 mM MgCl2; 1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1360.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.333α = 90
b = 94.333β = 90
c = 450.088γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9792,0.9611NSLSX29A

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
13.75099.90.06920.95.5240262011411
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)
13.73.8399.80.4024.55.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTPDB ENTRIES 2H1E,1Z63,1Z3I3.750129491294968899.940.264620.261860.31772RANDOM126.878
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]
3.441.723.44-5.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.411
r_dihedral_angle_3_deg24.559
r_dihedral_angle_4_deg20.41
r_dihedral_angle_1_deg8.405
r_angle_refined_deg1.628
r_chiral_restr0.111
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.411
r_dihedral_angle_3_deg24.559
r_dihedral_angle_4_deg20.41
r_dihedral_angle_1_deg8.405
r_angle_refined_deg1.628
r_chiral_restr0.111
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_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 Atoms5712
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
SOLVEphasing
SHARPphasing
PHENIXrefinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling