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Crystal Structures of Bacillus subtilis Alkaline Phytase in Complex with Ca2+, Co2+, Ni2+, Mg2+ and myo-Inositol Hexasulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H6L PDB ENTRY 1H6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 5mM CoCl2, 5mM NiCl2, 5mM MgCl2, 0.1M HEPES, 12% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.129 α = 90 b = 73.463 β = 90 c = 52.81 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2009-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.25 25 98.7 0.05 33.4 8.3 97536 96215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 95.5 0.359 4.3 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1H6L 1.25 23.95 97536 88095 4669 100 0.13898 0.13685 0.1324 0.17805 0.1714 RANDOM 29.6
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 -0.59 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 17.115 r_dihedral_angle_3_deg 12.614 r_scangle_it 7.863 r_dihedral_angle_1_deg 7.431 r_scbond_it 5.613 r_mcangle_it 4.11 r_rigid_bond_restr 3.109 r_mcbond_it 2.95 r_angle_refined_deg 2.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 17.115 r_dihedral_angle_3_deg 12.614 r_scangle_it 7.863 r_dihedral_angle_1_deg 7.431 r_scbond_it 5.613 r_mcangle_it 4.11 r_rigid_bond_restr 3.109 r_mcbond_it 2.95 r_angle_refined_deg 2.288 r_chiral_restr 0.161 r_bond_refined_d 0.021 r_gen_planes_refined 0.015 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 Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 781 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing REFMAC refinement