X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D4L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1141.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.191α = 90
b = 61.191β = 90
c = 63.31γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2004-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8031EMBL/DESY, HAMBURGX13

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
11.835397.370.0910.0748.852.741163711637-333.38
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)
11.831.9495.040.5030.42.662.541804

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2D4L1.8520107391073961198.010.161940.161940.160220.19193RANDOM32.784
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]
1.10.551.1-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.375
r_dihedral_angle_4_deg20.842
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg12.098
r_scangle_it11.383
r_scbond_it8.758
r_mcangle_it4.382
r_mcbond_it3.232
r_angle_refined_deg1.862
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.375
r_dihedral_angle_4_deg20.842
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg12.098
r_scangle_it11.383
r_scbond_it8.758
r_mcangle_it4.382
r_mcbond_it3.232
r_angle_refined_deg1.862
r_nbtor_refined0.319
r_nbd_refined0.23
r_symmetry_vdw_refined0.213
r_xyhbond_nbd_refined0.187
r_symmetry_hbond_refined0.148
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms812
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling