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X-Ray structure of the putative gluconolactonase in protein family PF08450. Northeast Structural Genomics Consortium target DrR130.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 0.1M NaCl
0.1M TOPS 18% PEG 3350, MgL2 as additive, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.42 α = 90 b = 93.4 β = 98.67 c = 76.99 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 100 CCD ADSC QUANTUM 4 mirror 2008-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 2.01 50 99.4 0.087 15.4 12.1 81184 -3
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 2.01 2.08 99.3 0.368 4.8
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 SAD THROUGHOUT 2.01 19.92 35195 1867 100 0.19466 0.19282 0.1938 0.22908 0.2315 RANDOM 26.406
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] 3.69 0.76 -2.5 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 6.238 r_scangle_it 2.642 r_scbond_it 1.692 r_angle_refined_deg 1.301 r_mcangle_it 1.118 r_mcbond_it 0.754 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_3_deg 13.881 r_dihedral_angle_1_deg 6.238 r_scangle_it 2.642 r_scbond_it 1.692 r_angle_refined_deg 1.301 r_mcangle_it 1.118 r_mcbond_it 0.754 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 4490 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling SnB phasing