X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZD9pdb entries 1zd9, 2H16
experimental modelPDB 2H16pdb entries 1zd9, 2H16

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52912M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.160.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.058α = 90
b = 134.885β = 90
c = 63.884γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
123097.90.04317.65.346561
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)
22.0796.20.5995.2

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 REPLACEMENTTHROUGHOUTpdb entries 1zd9, 2H1623046505177797.8890.2070.207490.20590.2453thin shells34.198
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]
-1.232.829-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.772
r_dihedral_angle_4_deg21.932
r_dihedral_angle_3_deg12.527
r_dihedral_angle_1_deg6.112
r_mcangle_it3.699
r_scangle_it3.102
r_mcbond_it2.54
r_scbond_it2.274
r_angle_refined_deg1.393
r_angle_other_deg1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.772
r_dihedral_angle_4_deg21.932
r_dihedral_angle_3_deg12.527
r_dihedral_angle_1_deg6.112
r_mcangle_it3.699
r_scangle_it3.102
r_mcbond_it2.54
r_scbond_it2.274
r_angle_refined_deg1.393
r_angle_other_deg1.039
r_mcbond_other0.59
r_symmetry_vdw_other0.242
r_symmetry_vdw_refined0.199
r_nbd_refined0.196
r_nbd_other0.191
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.128
r_metal_ion_refined0.092
r_chiral_restr0.08
r_nbtor_other0.079
r_symmetry_hbond_refined0.067
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3918
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms108

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction