1P47 | pdb_00001p47

Crystal Structure of tandem Zif268 molecules complexed to DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AAYPDB ENTRY 1AAY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298bis-tris propane-HCl, sodium chloride, zinc cloride, ammonium acetate, PEG 400, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.2170.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.629α = 90
b = 70.629β = 90
c = 99.608γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 42002-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
12.210090.40.04727.94.42574824823-2-2
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)
2.22.28430.4052.121243

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AAY2.260.862239322393242990.40.21920.21920.213940.230.267430.27RANDOM62.044
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]
-0.05-0.03-0.050.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.907
r_scangle_it7.14
r_scbond_it5.245
r_angle_refined_deg4.433
r_mcangle_it3.239
r_mcbond_it1.883
r_angle_other_deg1.616
r_nbd_other0.296
r_symmetry_vdw_other0.245
r_nbd_refined0.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.907
r_scangle_it7.14
r_scbond_it5.245
r_angle_refined_deg4.433
r_mcangle_it3.239
r_mcbond_it1.883
r_angle_other_deg1.616
r_nbd_other0.296
r_symmetry_vdw_other0.245
r_nbd_refined0.244
r_xyhbond_nbd_refined0.241
r_chiral_restr0.215
r_symmetry_vdw_refined0.16
r_nbtor_other0.118
r_symmetry_hbond_refined0.105
r_bond_refined_d0.045
r_gen_planes_refined0.021
r_gen_planes_other0.013
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1431
Nucleic Acid Atoms896
Solvent Atoms100
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing