X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BHDPDB ENTRY 3BHD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.81.6 M NA/K PHOSPHATE PH 6.8
Crystal Properties
Matthews coefficientSolvent content
3.4964.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.181α = 90
b = 93.578β = 93.04
c = 70.775γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.170.6899.50.0619.344.5839110-3
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)
12.12.2398.30.582.364.49

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3BHD2.170.6837148196399.530.212320.211250.23199RANDOM52.162
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]
-1.121.2-0.481.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg16.319
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg6.063
r_angle_refined_deg1.518
r_mcangle_it1.292
r_scbond_it1.006
r_angle_other_deg0.933
r_mcbond_it0.726
r_mcbond_other0.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg16.319
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg6.063
r_angle_refined_deg1.518
r_mcangle_it1.292
r_scbond_it1.006
r_angle_other_deg0.933
r_mcbond_it0.726
r_mcbond_other0.726
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3000
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing