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Crystal structure of Predicted metal-dependent phosphohydrolase (ZP_00055740.2) from Magnetospirillum magnetotacticum MS-1 at 1.37 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.67 277 20.0000% polyethylene glycol 3000, 0.2500M calcium acetate, 0.1M TRIS pH 7.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.852 α = 90 b = 83.906 β = 116.89 c = 71.278 γ = 90
Symmetry Space Group C 1 2 1
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 VERTICAL FOCUSING MIRROR 2009-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.37 41.959 99.2 85080 -3 12.68
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) 1.37 1.42 97.3 0.495 2.2
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) 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) Mean Isotropic B X-RAY DIFFRACTION SAD 1.37 41.96 85080 4252 99.5 0.133 0.132 0.1521 0.164 0.1794 19.47
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] -1.02 -0.18 1.15 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.029 r_dihedral_angle_4_deg 12.976 r_dihedral_angle_1_deg 4.521 r_scangle_it 3.155 r_scbond_it 2.114 r_mcangle_it 1.236 r_angle_refined_deg 1.147 r_angle_other_deg 0.905 r_mcbond_it 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.029 r_dihedral_angle_4_deg 12.976 r_dihedral_angle_1_deg 4.521 r_scangle_it 3.155 r_scbond_it 2.114 r_mcangle_it 1.236 r_angle_refined_deg 1.147 r_angle_other_deg 0.905 r_mcbond_it 0.776 r_rigid_bond_restr 0.736 r_mcbond_other 0.234 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3163 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction autoSHARP phasing