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Crystal structure of YrbI phosphatase from Escherichia coli
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 = 85.071 α = 90 b = 156.959 β = 96.54 c = 114.407 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 2007-04-13 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 2.6 39.8 86138
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 2.6 30 86138 4530 99.11 0.20291 0.20118 0.1996 0.2364 0.2335 RANDOM 54.162
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] 0.62 0.34 -0.48 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.793 r_dihedral_angle_4_deg 13.712 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 3.976 r_angle_refined_deg 0.864 r_scangle_it 0.725 r_scbond_it 0.408 r_mcangle_it 0.362 r_nbtor_refined 0.291 r_mcbond_it 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.793 r_dihedral_angle_4_deg 13.712 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 3.976 r_angle_refined_deg 0.864 r_scangle_it 0.725 r_scbond_it 0.408 r_mcangle_it 0.362 r_nbtor_refined 0.291 r_mcbond_it 0.196 r_nbd_refined 0.155 r_symmetry_vdw_refined 0.13 r_xyhbond_nbd_refined 0.105 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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 21566 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement