X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F9MPDB ENTRY 3F9M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2244.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.88α = 90
b = 82.12β = 90
c = 86.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2008-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0001SLSX06SA

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
12.152584.50.0760.06717.23.6262912223122
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)
12.152.2784.80.330.273.122741

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 3F9M2.1520222223121054112584.50.199770.196730.25529RANDOM19.864
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]
1.120.46-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.578
r_dihedral_angle_4_deg20.122
r_dihedral_angle_3_deg17.363
r_dihedral_angle_1_deg5.689
r_scangle_it2.635
r_scbond_it1.617
r_angle_refined_deg1.267
r_mcangle_it1.108
r_angle_other_deg0.923
r_mcbond_it0.583
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.578
r_dihedral_angle_4_deg20.122
r_dihedral_angle_3_deg17.363
r_dihedral_angle_1_deg5.689
r_scangle_it2.635
r_scbond_it1.617
r_angle_refined_deg1.267
r_mcangle_it1.108
r_angle_other_deg0.923
r_mcbond_it0.583
r_symmetry_vdw_other0.293
r_nbd_refined0.202
r_nbd_other0.201
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_other0.148
r_metal_ion_refined0.124
r_mcbond_other0.103
r_symmetry_vdw_refined0.101
r_nbtor_other0.086
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3512
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling