X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G8KPDB ENTRY 4G8K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72935 mM MgCl2, 5 mM DTT, 18% PEG2000, 100 mM NaCl, and 100 mM SPG buffer, pH 7. , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.197α = 90
b = 267.392β = 90.04
c = 110.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

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
12.559.295.70.1046.831063471.61.6
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)
12.5042.56988.40.5261.63.27277

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMR-SADTHROUGHOUTPDB ENTRY 4G8K2.559.21.6111125106347572595.670.19750.195680.23107RANDOM51.977
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]
2.951.86-18.3615.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.044
r_dihedral_angle_4_deg18.386
r_dihedral_angle_3_deg16.195
r_long_range_B_refined9.069
r_long_range_B_other9.065
r_dihedral_angle_1_deg5.394
r_scangle_other4.616
r_mcangle_it4.357
r_mcangle_other4.357
r_scbond_it2.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.044
r_dihedral_angle_4_deg18.386
r_dihedral_angle_3_deg16.195
r_long_range_B_refined9.069
r_long_range_B_other9.065
r_dihedral_angle_1_deg5.394
r_scangle_other4.616
r_mcangle_it4.357
r_mcangle_other4.357
r_scbond_it2.789
r_scbond_other2.788
r_mcbond_it2.695
r_mcbond_other2.692
r_angle_refined_deg1.231
r_angle_other_deg0.832
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21367
Nucleic Acid Atoms
Solvent Atoms1030
Heterogen Atoms432

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling