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Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.37 α = 90 b = 156.908 β = 96.54 c = 114.051 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 2.1 38.4 162029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 30 162029 8524 98.42 0.1863 0.18397 0.1848 0.23075 0.2314 RANDOM 35.509
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] 0.51 1.06 -0.3 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.384 r_dihedral_angle_4_deg 16.168 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 4.704 r_scangle_it 1.428 r_angle_refined_deg 1.045 r_scbond_it 0.877 r_mcangle_it 0.535 r_nbtor_refined 0.295 r_mcbond_it 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.384 r_dihedral_angle_4_deg 16.168 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_1_deg 4.704 r_scangle_it 1.428 r_angle_refined_deg 1.045 r_scbond_it 0.877 r_mcangle_it 0.535 r_nbtor_refined 0.295 r_mcbond_it 0.295 r_nbd_refined 0.178 r_metal_ion_refined 0.176 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21648 Nucleic Acid Atoms Solvent Atoms 2598 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement