X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E31 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52888% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.5952.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.12α = 90
b = 76.594β = 90
c = 193.939γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402006-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.697.199.50.06619.84.816474
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)
12.62.6599.60.3084.6

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 REPLACEMENTTHROUGHOUT2E312.660.081551682699.150.207670.204640.2656RANDOM56.529
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]
2.98-2.42-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_3_deg20.04
r_dihedral_angle_4_deg18.88
r_dihedral_angle_1_deg7.469
r_long_range_B_refined5.203
r_long_range_B_other5.202
r_scangle_other3.89
r_scbond_it2.73
r_scbond_other2.729
r_mcangle_it2.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_3_deg20.04
r_dihedral_angle_4_deg18.88
r_dihedral_angle_1_deg7.469
r_long_range_B_refined5.203
r_long_range_B_other5.202
r_scangle_other3.89
r_scbond_it2.73
r_scbond_other2.729
r_mcangle_it2.137
r_mcangle_other2.136
r_angle_refined_deg1.63
r_mcbond_other1.233
r_mcbond_it1.232
r_angle_other_deg0.87
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms3205
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling