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Crystal structure of putative dehydratase from Zymomonas mobilis ZM4
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 8.5 294 100mM Tris-HCl, pH 8.5, 30% PEG 4000, 200mM Lithium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.17 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.178 α = 90 b = 190.409 β = 90 c = 85.922 γ = 90
Symmetry Space Group P 21 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 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97960 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 1.8 50 100 0.094 0.075 4.8 6.7 288410 288410 -5 16.777
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 99.8 0.48 0.43 2.2 6.2 28540
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 (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 278981 278981 8758 99.64 0.14513 0.14513 0.14386 0.1444 0.18553 0.1854 RANDOM 18.369
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] -0.18 0.23 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 15.781 r_scangle_it 8.56 r_dihedral_angle_1_deg 7.896 r_scbond_it 6.099 r_mcangle_it 4.108 r_mcbond_it 3.18 r_angle_refined_deg 1.171 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.12 r_dihedral_angle_4_deg 18.864 r_dihedral_angle_3_deg 15.781 r_scangle_it 8.56 r_dihedral_angle_1_deg 7.896 r_scbond_it 6.099 r_mcangle_it 4.108 r_mcbond_it 3.18 r_angle_refined_deg 1.171 r_nbtor_refined 0.309 r_nbd_refined 0.181 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.157 r_symmetry_vdw_refined 0.155 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 24692 Nucleic Acid Atoms Solvent Atoms 3160 Heterogen Atoms 96
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling