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Crystal structure of mannonate dehydratase (target EFI-502209) from Caulobacter crescentus CB15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 0.1M BICINE, PH 9.0, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.12 41.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.302 α = 90 b = 116.302 β = 90 c = 118.078 γ = 90
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 2011-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.37 70 92.6 0.09 5.8 4.1 163715 -5 18.735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.39 98.3 0.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MR THROUGHOUT 3TW9 1.45 50 122475 3812 91.19 0.13221 0.13045 0.131 0.18819 0.1894 RANDOM 22.222
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] -0.77 -0.77 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_sphericity_free 23.534 r_dihedral_angle_4_deg 18.265 r_rigid_bond_restr 16.588 r_dihedral_angle_3_deg 13.069 r_sphericity_bonded 11.984 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.454 r_chiral_restr 0.097 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_sphericity_free 23.534 r_dihedral_angle_4_deg 18.265 r_rigid_bond_restr 16.588 r_dihedral_angle_3_deg 13.069 r_sphericity_bonded 11.984 r_dihedral_angle_1_deg 6.209 r_angle_refined_deg 1.454 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6312 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 32
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling