1N8N

Crystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3
Crystal Properties
Matthews coefficientSolvent content
3.3463.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.279α = 90
b = 92.457β = 90
c = 138.182γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal mirror2002-07-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.0377, 1.0404, 0.9392ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.6946.1388.80.0610.06173.7318843188419.709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.79530.0930.09371.62976

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMAD-phased Bromine derivative at 2.2 A resolution1.6946.133188431884167388.80.179060.179060.177590.20698RANDOM20.602
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]
1.63-0.72-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.605
r_scangle_it4.623
r_scbond_it2.695
r_mcangle_it1.634
r_angle_refined_deg1.412
r_mcbond_it0.898
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.223
r_nbd_refined0.197
r_xyhbond_nbd_refined0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.605
r_scangle_it4.623
r_scbond_it2.695
r_mcangle_it1.634
r_angle_refined_deg1.412
r_mcbond_it0.898
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.223
r_nbd_refined0.197
r_xyhbond_nbd_refined0.148
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1643
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms1

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling