X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5281.16100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K
Crystal Properties
Matthews coefficientSolvent content
2.9257.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.985α = 90
b = 48.985β = 90
c = 105.62γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92Rigaku VariMax HF Confocal Mirror2006-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.1544.4499.70.0958.97.34135721352623
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)
12.152.2399.50.6012.27.241334

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1544.46707439399.570.238340.234090.32073RANDOM38.072
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]
0.80.8-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.988
r_dihedral_angle_4_deg17.376
r_dihedral_angle_3_deg17.117
r_dihedral_angle_1_deg10.26
r_scangle_it7.613
r_scbond_it5.677
r_mcangle_it3.539
r_mcbond_it2.54
r_angle_refined_deg2.034
r_symmetry_vdw_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.988
r_dihedral_angle_4_deg17.376
r_dihedral_angle_3_deg17.117
r_dihedral_angle_1_deg10.26
r_scangle_it7.613
r_scbond_it5.677
r_mcangle_it3.539
r_mcbond_it2.54
r_angle_refined_deg2.034
r_symmetry_vdw_refined0.327
r_nbtor_refined0.313
r_nbd_refined0.235
r_xyhbond_nbd_refined0.211
r_symmetry_hbond_refined0.191
r_chiral_restr0.168
r_bond_refined_d0.023
r_gen_planes_refined0.008
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_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms760
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
d*TREKdata scaling