X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727716.5% PEG 2000, 0.1 M TRIS-HCL, 0.08% B-D-GLYCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3863.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.49α = 90
b = 136.49β = 90
c = 170.22γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9998APS22-ID

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
12.12094.90.06215.83.8100051
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)
12.12.1764.60.2943.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2EWD2.119.8891538488091.330.231570.231570.230310.25537RANDOM53.287
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]
1.371.371.37-4.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.918
r_dihedral_angle_4_deg14.519
r_dihedral_angle_3_deg11.179
r_dihedral_angle_1_deg4.607
r_angle_refined_deg0.844
r_angle_other_deg0.65
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.918
r_dihedral_angle_4_deg14.519
r_dihedral_angle_3_deg11.179
r_dihedral_angle_1_deg4.607
r_angle_refined_deg0.844
r_angle_other_deg0.65
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8905
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing