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Crystal structure of a member of enolase superfamily from Roseovarius nubinhibens ISM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 4M Sodium formate, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.39 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.842 α = 90 b = 126.842 β = 90 c = 96.608 γ = 90
Symmetry Space Group P 4 21 2
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 MAR CCD 165 mm MIRRORS 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9796 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 50 99.9 0.108 0.074 5.4 7.8 35405 35405 -5 42.941
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.72 0.64 1.5 7.7
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 2.3 20 33995 1098 99.34 0.18392 0.18243 0.1782 0.22844 0.2261 RANDOM 40.689
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] -1.69 -1.69 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.294 r_dihedral_angle_4_deg 21.388 r_dihedral_angle_3_deg 19.454 r_scangle_it 8.02 r_dihedral_angle_1_deg 7.889 r_scbond_it 5.512 r_mcangle_it 4.428 r_mcbond_it 3.063 r_angle_refined_deg 1.125 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.294 r_dihedral_angle_4_deg 21.388 r_dihedral_angle_3_deg 19.454 r_scangle_it 8.02 r_dihedral_angle_1_deg 7.889 r_scbond_it 5.512 r_mcangle_it 4.428 r_mcbond_it 3.063 r_angle_refined_deg 1.125 r_nbtor_refined 0.292 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.151 r_nbd_refined 0.13 r_symmetry_vdw_refined 0.106 r_chiral_restr 0.096 r_bond_refined_d 0.007 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_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 5556 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 12
Software Software Software Name Purpose SHELX model building REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHELX phasing