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Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G9I PDB entry 2G9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 25% PEG 5000 MME, 10 mM GDP, MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.367 α = 90 b = 98.367 β = 90 c = 94.347 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315 mirrors 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 APS 19-ID
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 1.35 40 98.7 0.055 22.3 8.2 99727 99727
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 1.35 1.37 97.9 0.49 4.69 7.5 4897
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 2G9I 1.35 40 99727 94754 4973 98.34 0.164 0.16179 0.1603 0.1692 0.18997 0.1973 RANDOM 15.446
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.187 r_dihedral_angle_4_deg 19.515 r_dihedral_angle_3_deg 12.472 r_dihedral_angle_1_deg 6.235 r_sphericity_free 5.961 r_scangle_it 3.703 r_sphericity_bonded 3.238 r_scbond_it 2.629 r_rigid_bond_restr 2.306 r_mcangle_it 2.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.187 r_dihedral_angle_4_deg 19.515 r_dihedral_angle_3_deg 12.472 r_dihedral_angle_1_deg 6.235 r_sphericity_free 5.961 r_scangle_it 3.703 r_sphericity_bonded 3.238 r_scbond_it 2.629 r_rigid_bond_restr 2.306 r_mcangle_it 2.009 r_angle_refined_deg 1.564 r_mcbond_it 1.493 r_angle_other_deg 0.955 r_mcbond_other 0.581 r_symmetry_vdw_other 0.333 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.226 r_symmetry_hbond_refined 0.218 r_nbd_other 0.206 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.092 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3809 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing