X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291Plate-like crystals were grown by hanging drop vapour diffusion with the drop consisting of 2 microliters of 15-20 mg/mL concentration protein, 10 mM sodium cacodylate in HCl buffer, pH 6.5 and 1 microliter of reservoir solution: 20% w/v PEG 4000, 0.1 M HEPES buffer, pH 7.5, 10% v/v isopropanol.
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.387α = 90
b = 151.411β = 117.11
c = 64.054γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm plate1998-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54178

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
11.92076.60.046229.25947759477-325.5
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)
11.91.9314.50.1285.4

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 DIFFRACTIONMIRFREE R-VALUE1.919.9759448300576.570.1250.128810.181Random selection14.619
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]
0.76-0.6-0.25-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.167
r_dihedral_angle_4_deg20.128
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.212
r_angle_refined_deg1.354
r_angle_other_deg0.791
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.167
r_dihedral_angle_4_deg20.128
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.212
r_angle_refined_deg1.354
r_angle_other_deg0.791
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7491
Nucleic Acid Atoms
Solvent Atoms1098
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
MOLREPphasing
XFITmodel building