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Crystal structure of YrbI phosphatase from Escherichia coli in a complex with Ca
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 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.578 α = 90 b = 156.947 β = 96.72 c = 113.991 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 1.85 36.61 231079
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 1.85 36.61 231079 12229 96.22 0.21499 0.21345 0.2132 0.24434 0.2447 RANDOM 27.832
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] -0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.72 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 5.121 r_scangle_it 2.359 r_scbond_it 1.443 r_angle_refined_deg 1.09 r_mcangle_it 0.889 r_mcbond_it 0.506 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.72 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 5.121 r_scangle_it 2.359 r_scbond_it 1.443 r_angle_refined_deg 1.09 r_mcangle_it 0.889 r_mcbond_it 0.506 r_nbtor_refined 0.3 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.19 r_metal_ion_refined 0.172 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.072 r_bond_refined_d 0.009 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 21549 Nucleic Acid Atoms Solvent Atoms 985 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement