X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E5EPDB entry 4E5E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1 M HEPES, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride
Crystal Properties
Matthews coefficientSolvent content
3.1861.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.395α = 90
b = 89.395β = 90
c = 134.14γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2014-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97921APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.985099.70.0730.0720.0148.92719228
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0596.80.9740.2330.80816.41831

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 4E5E1.98451823998499.590.18650.18480.2195RANDOM49.137
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]
0.40.4-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.241
r_dihedral_angle_4_deg16.609
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg7.469
r_mcangle_it3.946
r_mcbond_it2.912
r_mcbond_other2.912
r_angle_refined_deg2.451
r_angle_other_deg1.288
r_chiral_restr0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.241
r_dihedral_angle_4_deg16.609
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg7.469
r_mcangle_it3.946
r_mcbond_it2.912
r_mcbond_other2.912
r_angle_refined_deg2.451
r_angle_other_deg1.288
r_chiral_restr0.177
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1436
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing