X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JBVPDB ENTRY 2JBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
116-22% W/V PEG3350, 200 MM MAGNESIUM FORMATE
Crystal Properties
Matthews coefficientSolvent content
1.9236

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.964α = 90
b = 120.907β = 91.39
c = 72.322γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)PETRA III, EMBL c/o DESYP13 (MX1)

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
11.95099.90.1596.967679
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)
11.91.9499.90.970.856.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JBV1.972.364121321899.790.180760.178050.23609RANDOM24.92
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]
3.77-0.11-0.9-2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.915
r_dihedral_angle_4_deg19.084
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg7.214
r_mcangle_it2.648
r_scbond_it2.44
r_angle_refined_deg1.858
r_mcbond_it1.853
r_mcbond_other1.853
r_angle_other_deg0.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.915
r_dihedral_angle_4_deg19.084
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg7.214
r_mcangle_it2.648
r_scbond_it2.44
r_angle_refined_deg1.858
r_mcbond_it1.853
r_mcbond_other1.853
r_angle_other_deg0.915
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.009
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_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 Atoms7861
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing