3AMR

Crystal Structures of Bacillus subtilis Alkaline Phytase in Complex with Ca2+, Co2+, Ni2+, Mg2+ and myo-Inositol Hexasulfate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H6LPDB ENTRY 1H6L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52985mM CoCl2, 5mM NiCl2, 5mM MgCl2, 0.1M HEPES, 12% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2344.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.129α = 90
b = 73.463β = 90
c = 52.81γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

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
11.252598.70.0533.48.39753696215
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)
11.251.2995.50.3594.36.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1H6L1.2523.95975368809546691000.138980.136850.17805RANDOM29.6
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]
0.44-0.590.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.279
r_dihedral_angle_4_deg17.115
r_dihedral_angle_3_deg12.614
r_scangle_it7.863
r_dihedral_angle_1_deg7.431
r_scbond_it5.613
r_mcangle_it4.11
r_rigid_bond_restr3.109
r_mcbond_it2.95
r_angle_refined_deg2.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.279
r_dihedral_angle_4_deg17.115
r_dihedral_angle_3_deg12.614
r_scangle_it7.863
r_dihedral_angle_1_deg7.431
r_scbond_it5.613
r_mcangle_it4.11
r_rigid_bond_restr3.109
r_mcbond_it2.95
r_angle_refined_deg2.288
r_chiral_restr0.161
r_bond_refined_d0.021
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms781
Heterogen Atoms47

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
REFMACrefinement