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Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M BIS-TRIS pH5.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.398 α = 90 b = 109.741 β = 90 c = 121.134 γ = 90
Symmetry Space Group P 21 21 21
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 mirrors 2011-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9783 NSLS X25
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 2.55 50 100 0.07 7.6 12.4 27367 27367
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 2.6 2.69 100 0.43 5 12.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.55 43.46 26367 25837 1360 97.16 0.22032 0.21741 0.2128 0.27739 0.2683 RANDOM 48.275
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] 0.07 -0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 20.178 r_dihedral_angle_1_deg 6.946 r_scangle_it 4.608 r_scbond_it 2.784 r_angle_refined_deg 1.88 r_mcangle_it 1.752 r_mcbond_it 0.911 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 20.178 r_dihedral_angle_1_deg 6.946 r_scangle_it 4.608 r_scbond_it 2.784 r_angle_refined_deg 1.88 r_mcangle_it 1.752 r_mcbond_it 0.911 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4402 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 25
Software Software Software Name Purpose CBASS data collection SHELXD phasing SHARP phasing CCP4 model building Coot model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing