X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H47 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52900.2 M magnesium chloride, 8% w/v PEG 20K, 8% v/v PEG 550 MME, 0.1 M TRIS pH 8.5, 3% w/v 1,5-diaminopentane dihydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.6653.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.21α = 90
b = 91.21β = 90
c = 56.34γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2013-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.04378.9998.10.1860.2030.0837.761703517035
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.14870.8430.8430.3870.95.52196

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 REPLACEMENTTHROUGHOUT3H472.04378.991703186499.650.19990.19790.2394RANDOM29.529
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.142
r_dihedral_angle_4_deg19.026
r_dihedral_angle_3_deg11.672
r_dihedral_angle_1_deg4.438
r_mcangle_it4.101
r_mcbond_it2.648
r_mcbond_other2.642
r_angle_refined_deg0.924
r_angle_other_deg0.715
r_chiral_restr0.049
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.142
r_dihedral_angle_4_deg19.026
r_dihedral_angle_3_deg11.672
r_dihedral_angle_1_deg4.438
r_mcangle_it4.101
r_mcbond_it2.648
r_mcbond_other2.642
r_angle_refined_deg0.924
r_angle_other_deg0.715
r_chiral_restr0.049
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1600
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms33

Software

Software
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction