X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H4E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), Mellitic acid (1mM). Mellitic acid stock was adjusted to pH 8.0 with TRIS prior to setting up trays.
Crystal Properties
Matthews coefficientSolvent content
2.6553.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.759α = 90
b = 90.759β = 90
c = 56.76γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2015-08-21MSINGLE 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 Merge I (Observed)Rpim I (All)CC (Half)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
11.9545.3897.90.1050.0430.99711.76.819152
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)
11.95299.50.8620.3680.6442.16.51357

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 REPLACEMENTTHROUGHOUT3H4E1.9545.381818896497.80.1950.19360.2206RANDOM31.245
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]
0.220.110.22-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.344
r_dihedral_angle_4_deg21.454
r_dihedral_angle_3_deg12.909
r_dihedral_angle_1_deg5.465
r_mcangle_it5.183
r_mcbond_it3.991
r_mcbond_other3.988
r_angle_refined_deg1.281
r_angle_other_deg0.899
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.344
r_dihedral_angle_4_deg21.454
r_dihedral_angle_3_deg12.909
r_dihedral_angle_1_deg5.465
r_mcangle_it5.183
r_mcbond_it3.991
r_mcbond_other3.988
r_angle_refined_deg1.281
r_angle_other_deg0.899
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1580
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms24

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction