X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.7 M sodium malonate, 100 mM Tris-HCl (pH 7.5)
Crystal Properties
Matthews coefficientSolvent content
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 189.026α = 90
b = 189.026β = 90
c = 157.181γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702014-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

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
11.45099.90.0646.37.3209648209344-3
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)
11.41.421000.415.97.2

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 DIFFRACTIONSADTHROUGHOUT1.4201982501056899.560.1550.1540.175RANDOM15.897
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]
-0.05-0.03-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.981
r_long_range_B_other4.498
r_scangle_other2.355
r_mcangle_it1.59
r_mcangle_other1.59
r_scbond_it1.469
r_scbond_other1.469
r_angle_refined_deg1.394
r_mcbond_it0.991
r_mcbond_other0.989
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined4.981
r_long_range_B_other4.498
r_scangle_other2.355
r_mcangle_it1.59
r_mcangle_other1.59
r_scbond_it1.469
r_scbond_other1.469
r_angle_refined_deg1.394
r_mcbond_it0.991
r_mcbond_other0.989
r_angle_other_deg0.775
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7466
Nucleic Acid Atoms
Solvent Atoms1222
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing