X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4148.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.498α = 90
b = 117.26β = 90
c = 68.801γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.000ALS8.2.2

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
12.655098.50.0763.1146502
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)
12.652.7492.10.2794.23

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 REPLACEMENTTHROUGHOUTPDB entry 3EKH2.6545.451391473698.270.225110.222290.2795RANDOM43.902
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]
-0.69-2.563.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.716
r_dihedral_angle_3_deg18.553
r_dihedral_angle_4_deg17.016
r_dihedral_angle_1_deg6.317
r_scangle_it2.569
r_scbond_it1.526
r_angle_refined_deg1.336
r_mcangle_it1.122
r_mcbond_it0.609
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.716
r_dihedral_angle_3_deg18.553
r_dihedral_angle_4_deg17.016
r_dihedral_angle_1_deg6.317
r_scangle_it2.569
r_scbond_it1.526
r_angle_refined_deg1.336
r_mcangle_it1.122
r_mcbond_it0.609
r_nbtor_refined0.302
r_nbd_refined0.204
r_symmetry_vdw_refined0.145
r_xyhbond_nbd_refined0.135
r_metal_ion_refined0.132
r_symmetry_hbond_refined0.13
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_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 Atoms2767
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms3

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection