X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSeMet EED structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82914M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6753.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.803α = 90
b = 85.337β = 90
c = 91.231γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDVertically collimating premirror, double crystal Si(111) monochromator with sagital focussing, vertical focusing mirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.9790SRSPX10.1

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
11.953098.50.0910.09114.54.431920319202
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)
1.952.02910.4260.4262.13.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSeMet EED structure1.9527.563144231442168098.550.197240.197240.195390.23156RANDOM21.715
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]
-0.02-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg14.369
r_dihedral_angle_1_deg7.254
r_scangle_it4.087
r_scbond_it2.737
r_mcangle_it1.782
r_angle_refined_deg1.68
r_mcbond_it1.15
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg14.369
r_dihedral_angle_1_deg7.254
r_scangle_it4.087
r_scbond_it2.737
r_mcangle_it1.782
r_angle_refined_deg1.68
r_mcbond_it1.15
r_nbtor_refined0.301
r_nbd_refined0.204
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.145
r_symmetry_hbond_refined0.124
r_chiral_restr0.119
r_bond_refined_d0.021
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2895
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms12

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling