X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52931.4M (NH4)2SO4, 50MM HEPES-NA PH 7
Crystal Properties
Matthews coefficientSolvent content
2.1743.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.397α = 90
b = 140.965β = 101.67
c = 81.297γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273CCDADSC QUANTUM 315r2013-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979526ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.0345.3990.80.1212.15327837337.46
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)
13.033.2184.50.433.012.9

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 REPLACEMENTTHROUGHOUT3PBN3.0345.3925070276691.030.254670.250970.28766RANDOM51.474
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]
2.33-0.46-4.121.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.637
r_dihedral_angle_4_deg16.581
r_dihedral_angle_3_deg15.326
r_dihedral_angle_1_deg6.492
r_long_range_B_refined5.99
r_long_range_B_other5.99
r_mcangle_it3.62
r_mcangle_other3.62
r_scangle_other3.277
r_mcbond_it2.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.637
r_dihedral_angle_4_deg16.581
r_dihedral_angle_3_deg15.326
r_dihedral_angle_1_deg6.492
r_long_range_B_refined5.99
r_long_range_B_other5.99
r_mcangle_it3.62
r_mcangle_other3.62
r_scangle_other3.277
r_mcbond_it2.081
r_mcbond_other2.081
r_scbond_it1.847
r_scbond_other1.84
r_angle_refined_deg1.268
r_angle_other_deg0.819
r_chiral_restr0.07
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 Atoms8332
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing