X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% (w/v) PEGMME 5K, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.7655

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.342α = 90
b = 95.714β = 115.59
c = 54.734γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 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
11.7547.8691.70.0670.9949.92.24050812.42
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)
11.751.85630.3280.7392.31.9

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 REPLACEMENTTHROUGHOUT1SPV1.7547.8637246320391.440.172470.170290.19833RANDOM19.392
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]
-8.08-0.8813.35-5.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_3_deg12.785
r_dihedral_angle_4_deg12.112
r_dihedral_angle_1_deg6.069
r_long_range_B_refined3.731
r_long_range_B_other3.608
r_scangle_other2.215
r_mcangle_it1.68
r_mcangle_other1.679
r_angle_refined_deg1.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.369
r_dihedral_angle_3_deg12.785
r_dihedral_angle_4_deg12.112
r_dihedral_angle_1_deg6.069
r_long_range_B_refined3.731
r_long_range_B_other3.608
r_scangle_other2.215
r_mcangle_it1.68
r_mcangle_other1.679
r_angle_refined_deg1.556
r_scbond_it1.372
r_scbond_other1.368
r_mcbond_it1.029
r_mcbond_other1.028
r_angle_other_deg0.94
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2911
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing