X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SPV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% (w/v) PEGMME 5K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.5852.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.368α = 90
b = 96.696β = 115.84
c = 54.353γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MKB mirrors2013-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9794ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
11.7748.9597.20.0660.99713.13.64138117.263
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8784.10.470.7432.22.8

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 REPLACEMENTTHROUGHOUT1SPV1.7748.3539295200397.10.152580.151790.16873RANDOM24.014
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]
-7.47-0.5414.43-6.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg18.418
r_dihedral_angle_3_deg13.76
r_dihedral_angle_1_deg5.958
r_long_range_B_refined4.956
r_long_range_B_other4.791
r_scangle_other3.291
r_scbond_it2.106
r_scbond_other2.105
r_mcangle_it2.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg18.418
r_dihedral_angle_3_deg13.76
r_dihedral_angle_1_deg5.958
r_long_range_B_refined4.956
r_long_range_B_other4.791
r_scangle_other3.291
r_scbond_it2.106
r_scbond_other2.105
r_mcangle_it2.078
r_mcangle_other2.078
r_angle_refined_deg1.722
r_mcbond_it1.373
r_mcbond_other1.371
r_angle_other_deg1.127
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2912
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing