X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XEFpdb entry 1XEF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6277sodium malonate, PEG 5500-MME, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.558α = 90
b = 195.166β = 110.85
c = 63.288γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.62096.40.05710.22537924465
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6593.20.193

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1XEF2.6203.22573824465129896.40.211470.207780.27936RANDOM15.404
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]
4.53-0.07-0.36-4.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.184
r_dihedral_angle_4_deg20.385
r_dihedral_angle_3_deg17.915
r_dihedral_angle_1_deg5.3
r_angle_refined_deg1.085
r_scangle_it0.925
r_scbond_it0.552
r_mcangle_it0.492
r_mcbond_it0.276
r_nbd_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.184
r_dihedral_angle_4_deg20.385
r_dihedral_angle_3_deg17.915
r_dihedral_angle_1_deg5.3
r_angle_refined_deg1.085
r_scangle_it0.925
r_scbond_it0.552
r_mcangle_it0.492
r_mcbond_it0.276
r_nbd_refined0.199
r_symmetry_hbond_refined0.177
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.149
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7552
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing