3LD3

Crystal structure of inorganic phosphatase from anaplasma phagocytophilum at 1.75a resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2290JCSG+ SCREEN CONDITION C6: 100MM PHOSPHATE/CITRATE PH 4.2, 40% PEG 300; ANPHA.01382.A AT 45MG/ ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.3647.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.38α = 90
b = 135.38β = 90
c = 135.38γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSingle crystal, cylindrically bent, Si(220)2009-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

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
11.752099.50.04830.2410.54159241385-330.82
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)
11.751.899.90.5293.78.83040

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3FQ3 MODIFIED WITH CCP4 PROGRAM CHAINSAW1.7519.964159241385206299.60.1610.1610.160.182RANDOM12.61
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
r_dihedral_angle_2_deg32.905
r_dihedral_angle_4_deg21.809
r_dihedral_angle_3_deg12.697
r_dihedral_angle_1_deg5.646
r_scangle_it3.793
r_scbond_it2.322
r_mcangle_it1.678
r_angle_refined_deg1.361
r_mcbond_it0.923
r_angle_other_deg0.883
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.905
r_dihedral_angle_4_deg21.809
r_dihedral_angle_3_deg12.697
r_dihedral_angle_1_deg5.646
r_scangle_it3.793
r_scbond_it2.322
r_mcangle_it1.678
r_angle_refined_deg1.361
r_mcbond_it0.923
r_angle_other_deg0.883
r_mcbond_other0.22
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2597
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms10

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling