3BDF

Crystal structure of metal-free E. coli alkaline phosphatase (T155V)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES, 0.2 M LiSO4, 1 mM ZnCl2, 5 mM MgCl2, 25-30% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.503α = 90
b = 103.634β = 105.8
c = 88.55γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Vertical focusing mirror, single crystal (Si111) bent monochromator (horizontal focusing)2007-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.00SSRLBL7-1

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
11.4500.05121.73.2210186
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)
1.41.450.3332.12

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 1ED91.450183759918497.260.1630.1620.184RANDOM15.036
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]
0.16-0.39-0.18-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_dihedral_angle_4_deg16.89
r_dihedral_angle_3_deg12.242
r_dihedral_angle_1_deg6.102
r_scangle_it3.669
r_scbond_it2.355
r_mcangle_it1.518
r_angle_refined_deg1.51
r_mcbond_it0.936
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_dihedral_angle_4_deg16.89
r_dihedral_angle_3_deg12.242
r_dihedral_angle_1_deg6.102
r_scangle_it3.669
r_scbond_it2.355
r_mcangle_it1.518
r_angle_refined_deg1.51
r_mcbond_it0.936
r_nbtor_refined0.301
r_nbd_refined0.207
r_symmetry_hbond_refined0.196
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.137
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6577
Nucleic Acid Atoms
Solvent Atoms1222
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing