X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F5V3F5V, 3RVV
experimental modelPDB 3RVV3F5V, 3RVV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.1M HEPES, 10% W/V PEG4000, 0.05M GLYGLYGLY, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.109α = 90
b = 59.377β = 90
c = 236.967γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.55092.60.0880.08824.86.323380-355.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5487.60.5960.5962.75.3

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 REPLACEMENTTHROUGHOUT3F5V, 3RVV2.55022108119491.80.180.1780.229RANDOM55.2
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]
-0.91.84-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg16.418
r_dihedral_angle_1_deg6.854
r_scangle_it2.903
r_scbond_it1.869
r_angle_refined_deg1.479
r_mcangle_it1.054
r_angle_other_deg0.885
r_mcbond_it0.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_dihedral_angle_4_deg18.035
r_dihedral_angle_3_deg16.418
r_dihedral_angle_1_deg6.854
r_scangle_it2.903
r_scbond_it1.869
r_angle_refined_deg1.479
r_mcangle_it1.054
r_angle_other_deg0.885
r_mcbond_it0.564
r_mcbond_other0.13
r_chiral_restr0.081
r_bond_refined_d0.015
r_bond_other_d0.006
r_gen_planes_refined0.006
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_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 Atoms5038
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
Cootmodel building