X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JTZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52940.1M sodium di-hydrogen phosphate, 2M sodium chloride, 0.1M potassium di-hydrogen phosphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
4.6873.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.225α = 90
b = 121.225β = 90
c = 94.995γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-14MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 225 mm CCD2007-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9395ESRFID14-4
2SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
1,22.8301000.19118.616.318587-1
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)
2.82.91000.9952.913.81970

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 REPLACEMENTTHROUGHOUT1JTZ2.8301795699599.740.175410.173880.20504RANDOM58.14
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]
2.211.12.21-3.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg19.316
r_dihedral_angle_3_deg13.798
r_dihedral_angle_1_deg5.741
r_scangle_it3.691
r_scbond_it2.353
r_mcangle_it2.271
r_mcbond_it1.203
r_angle_refined_deg0.999
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg19.316
r_dihedral_angle_3_deg13.798
r_dihedral_angle_1_deg5.741
r_scangle_it3.691
r_scbond_it2.353
r_mcangle_it2.271
r_mcbond_it1.203
r_angle_refined_deg0.999
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2494
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms5

Software

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