3BBB

Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG 1500, 50 mM sodium citrate, 20 mM MgCl2, 5 mM DTT, Crystals soaked with 10 mM d(AG), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
1.9235.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.466α = 90
b = 118.219β = 90
c = 128.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9000APS14-BM-C

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
11.32799.30.08616.48195789195789
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)
1.31.3598.30.422.36.8

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 REPLACEMENTTHROUGHOUTpdb entry 1NUE1.327183782967898.180.176960.174690.22025RANDOM14.161
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]
0.110.21-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.612
r_dihedral_angle_4_deg21.777
r_dihedral_angle_3_deg13.714
r_sphericity_free10.771
r_dihedral_angle_1_deg6.384
r_sphericity_bonded5.741
r_scangle_it4.791
r_scbond_it3.688
r_mcangle_it2.699
r_rigid_bond_restr2.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.612
r_dihedral_angle_4_deg21.777
r_dihedral_angle_3_deg13.714
r_sphericity_free10.771
r_dihedral_angle_1_deg6.384
r_sphericity_bonded5.741
r_scangle_it4.791
r_scbond_it3.688
r_mcangle_it2.699
r_rigid_bond_restr2.399
r_mcbond_it2.265
r_angle_refined_deg1.885
r_mcbond_other1.237
r_angle_other_deg1.202
r_nbd_refined0.227
r_nbd_other0.215
r_symmetry_vdw_other0.21
r_nbtor_refined0.187
r_chiral_restr0.187
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.137
r_nbtor_other0.084
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7218
Nucleic Acid Atoms
Solvent Atoms641
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing