X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FVNPDB ENTRY 3FVN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.530335% PEG3350, 0.3M LiSO4, 5mM MSVIII-19, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.627α = 80.41
b = 50.86β = 84.16
c = 62.931γ = 62.06
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95IMAGE PLATEMAR scanner 345 mm plate2008-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.9SPring-8BL26B2

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
11.55096.90.04323.97995279952
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5593.80.2654.543.57699

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 3FVN1.527.2475825400296.950.169250.168020.19184RANDOM13.632
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]
0.05-0.020.1-0.31-0.070.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.093
r_dihedral_angle_3_deg12.372
r_dihedral_angle_4_deg11.931
r_dihedral_angle_1_deg5.562
r_scangle_it2.702
r_scbond_it1.793
r_angle_refined_deg1.266
r_mcangle_it1.117
r_mcbond_it0.765
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.093
r_dihedral_angle_3_deg12.372
r_dihedral_angle_4_deg11.931
r_dihedral_angle_1_deg5.562
r_scangle_it2.702
r_scbond_it1.793
r_angle_refined_deg1.266
r_mcangle_it1.117
r_mcbond_it0.765
r_nbtor_refined0.308
r_nbd_refined0.197
r_symmetry_vdw_refined0.173
r_symmetry_hbond_refined0.123
r_xyhbond_nbd_refined0.104
r_chiral_restr0.084
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4103
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms104

Software

Software
Software NamePurpose
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing