X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UPG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.2 M sodium acetate, 0.1 M MES, 28% w/v 400 PEG
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.723α = 90
b = 153.84β = 102.32
c = 66.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2014-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97949DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.5549.49970.0370.99.83.9171689
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.55950.5550.51.44

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 REPLACEMENTTHROUGHOUT3UPG1.5549.49163191844597.110.171720.170290.19929RANDOM23.584
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]
0.81-0.03-0.45-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.847
r_dihedral_angle_4_deg15.589
r_dihedral_angle_3_deg11.967
r_dihedral_angle_1_deg6.796
r_long_range_B_refined6.559
r_long_range_B_other6.559
r_scangle_other5.284
r_scbond_it3.566
r_scbond_other3.565
r_mcangle_it3.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.847
r_dihedral_angle_4_deg15.589
r_dihedral_angle_3_deg11.967
r_dihedral_angle_1_deg6.796
r_long_range_B_refined6.559
r_long_range_B_other6.559
r_scangle_other5.284
r_scbond_it3.566
r_scbond_other3.565
r_mcangle_it3.119
r_mcangle_other3.119
r_mcbond_it2.285
r_mcbond_other2.284
r_angle_refined_deg2.149
r_angle_other_deg1.046
r_chiral_restr0.134
r_bond_refined_d0.023
r_gen_planes_refined0.012
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 Atoms7301
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing