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Crystal Structure of the T. brucei enolase complexed with phosphonoacetohydroxamate (PAH), His156-out conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 10 % (w/v) PEG1000, 0.01 M ZnSO4 or ZnCl2, and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.858 α = 90 b = 109.279 β = 90 c = 107.946 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm MIRRORS 2003-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.42 LNLS D03B-MX1
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 1.65 28 95.5 0.055 26.4 8.3 52580 50214 1 1
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) 1.65 1.74 91.4 0.409 3.9 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1OEP 1.65 27.95 50064 47566 2554 95.01 0.16692 0.16501 0.1597 0.20344 0.2022 RANDOM 29.621
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 -0.05 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.818 r_dihedral_angle_4_deg 19.007 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_1_deg 6.565 r_scangle_it 4.628 r_scbond_it 2.918 r_mcangle_it 2.342 r_angle_refined_deg 1.668 r_mcbond_it 1.501 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.818 r_dihedral_angle_4_deg 19.007 r_dihedral_angle_3_deg 13.583 r_dihedral_angle_1_deg 6.565 r_scangle_it 4.628 r_scbond_it 2.918 r_mcangle_it 2.342 r_angle_refined_deg 1.668 r_mcbond_it 1.501 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.106 r_metal_ion_refined 0.072 r_symmetry_metal_ion_refined 0.023 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_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 3288 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling MOLREP phasing