X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72911.4M malonate, pH 7, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
679.3
679.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.62α = 90
b = 107.62β = 90
c = 82.995γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.63099.80.1218.320.99139
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)
12.62.6999.40.9421.3

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 1wln2.60230911942399.7810.2160.2160.21470.243340.806
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]
2.3941.1972.394-3.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.279
r_dihedral_angle_4_deg17.117
r_dihedral_angle_3_deg16.144
r_dihedral_angle_1_deg6.947
r_mcangle_it4.145
r_scangle_it3.697
r_mcbond_it3.427
r_scbond_it2.667
r_angle_refined_deg1.365
r_angle_other_deg0.839
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.279
r_dihedral_angle_4_deg17.117
r_dihedral_angle_3_deg16.144
r_dihedral_angle_1_deg6.947
r_mcangle_it4.145
r_scangle_it3.697
r_mcbond_it3.427
r_scbond_it2.667
r_angle_refined_deg1.365
r_angle_other_deg0.839
r_mcbond_other0.467
r_symmetry_vdw_refined0.42
r_symmetry_vdw_other0.288
r_nbd_refined0.208
r_nbd_other0.195
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.13
r_symmetry_metal_ion_refined0.095
r_nbtor_other0.088
r_chiral_restr0.078
r_symmetry_hbond_refined0.068
r_bond_refined_d0.015
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms814
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms3

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction