X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DFO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52940.1M Hepes (N-(2-hydroxylethyl)piperazine-N -2 ethansulfonic acid) pH 7.5, 1.4M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4148.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.59α = 90
b = 112.59β = 90
c = 68.929γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.97623BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.350940.139.74.36600
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.4297.30.482.54.3734

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 REPLACEMENTTHROUGHOUT1dfo3.350635631994.760.256250.255280.27535RANDOM39.946
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]
3.173.17-6.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_3_deg14.009
r_dihedral_angle_4_deg3.504
r_dihedral_angle_1_deg3.404
r_angle_refined_deg0.776
r_nbtor_refined0.284
r_nbd_refined0.134
r_symmetry_vdw_refined0.095
r_scangle_it0.089
r_xyhbond_nbd_refined0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_3_deg14.009
r_dihedral_angle_4_deg3.504
r_dihedral_angle_1_deg3.404
r_angle_refined_deg0.776
r_nbtor_refined0.284
r_nbd_refined0.134
r_symmetry_vdw_refined0.095
r_scangle_it0.089
r_xyhbond_nbd_refined0.066
r_scbond_it0.051
r_chiral_restr0.05
r_mcangle_it0.04
r_symmetry_hbond_refined0.031
r_mcbond_it0.022
r_bond_refined_d0.005
r_gen_planes_refined0.001
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3185
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement