1HD7

A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.50.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.
Crystal Properties
Matthew coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.39α = 90
b = 44.85β = 124.54
c = 78.14γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDDUAL CRYSTAL MIRROR1999-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-5SSRLBL1-5

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
11.952599.40.0826.63.33490529.68
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)
11.952.0199.20.471.53.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTTO BE PUBLISHED1.952526771269992.20.2050.255RANDOM37.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.7
p_staggered_tor18.1
p_planar_tor8.4
p_scangle_it3.4
p_mcangle_it2.7
p_scbond_it2.2
p_mcbond_it1.8
p_multtor_nbd0.261
p_singtor_nbd0.185
p_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.7
p_staggered_tor18.1
p_planar_tor8.4
p_scangle_it3.4
p_mcangle_it2.7
p_scbond_it2.2
p_mcbond_it1.8
p_multtor_nbd0.261
p_singtor_nbd0.185
p_chiral_restr0.15
p_xyhbond_nbd0.125
p_planar_d0.069
p_angle_d0.038
p_plane_restr0.03
p_bond_d0.016
p_xhyhbond_nbd
p_hb_or_metal_coord
p_orthonormal_tor
p_angle_deg
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2070
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing