X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EFAPDB entry 1EFA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52811.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
5.0375.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 253.08α = 90
b = 253.08β = 90
c = 203.247γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic mirrors2006-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
13.52099.890.1760.1767.39.13134229717-3-325.4
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)
3.53.699.70.5040.5044.376.92090

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 REPLACEMENTTHROUGHOUTPDB entry 1EFA3.519.982971729717158199.860.236160.236160.233470.28656RANDOM53.844
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]
-0.02-0.01-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_dihedral_angle_3_deg20.917
r_dihedral_angle_4_deg17.201
r_dihedral_angle_1_deg5.896
r_scangle_it1.752
r_angle_refined_deg1.627
r_mcangle_it0.983
r_scbond_it0.927
r_mcbond_it0.551
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_dihedral_angle_3_deg20.917
r_dihedral_angle_4_deg17.201
r_dihedral_angle_1_deg5.896
r_scangle_it1.752
r_angle_refined_deg1.627
r_mcangle_it0.983
r_scbond_it0.927
r_mcbond_it0.551
r_nbtor_refined0.308
r_nbd_refined0.224
r_chiral_restr0.145
r_symmetry_vdw_refined0.144
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.108
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7418
Nucleic Acid Atoms1046
Solvent Atoms
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing