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Crystal structure of a member of the enolase superfamily from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL5 PDB entry 2GL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 100MM SODIUM CACODYLATE, PH 6.5, 2M AMMONIUM SULFATE, 100MM NACL, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 3.28 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.071 α = 90 b = 102.071 β = 90 c = 369.202 γ = 120
Symmetry Space Group P 65 2 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 ADSC QUANTUM 315 MIRRORS 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.072 NSLS X29A
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 1.8 50 99.8 0.068 0.064 11.7 6.2 106184 106184
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 1.8 1.86 99 0.46 0.41 2.4 3.8 10308
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2GL5 1.8 20 -5 102915 102915 3183 99.72 0.17036 0.17036 0.16937 0.1704 0.20144 0.2006 RANDOM 27.165
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] 0.4 0.2 0.4 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 15.174 r_dihedral_angle_3_deg 14.573 r_scangle_it 8.432 r_dihedral_angle_1_deg 6.96 r_scbond_it 5.861 r_mcangle_it 4.247 r_mcbond_it 3.319 r_angle_refined_deg 1.361 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_dihedral_angle_4_deg 15.174 r_dihedral_angle_3_deg 14.573 r_scangle_it 8.432 r_dihedral_angle_1_deg 6.96 r_scbond_it 5.861 r_mcangle_it 4.247 r_mcbond_it 3.319 r_angle_refined_deg 1.361 r_nbtor_refined 0.301 r_metal_ion_refined 0.256 r_symmetry_hbond_refined 0.244 r_chiral_restr 0.196 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_refined 0.144 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_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 5968 Nucleic Acid Atoms Solvent Atoms 895 Heterogen Atoms 111
Software Software Software Name Purpose MOLREP phasing REFMAC refinement ADSC data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing