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Crystal structure of phosphoribosylamine-glycine ligase from Ehrlichia chaffeensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YS7 pdb deposition 2ys7 modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 HR INDEX SCREEN F2: 100MM TRIS PH 8.5, 20% PEG 2000 MME, 200MM TRIMETHYLAMINE-N-OXIDE; EHCHA.00685.A AT 22.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.85 α = 90 b = 74.16 β = 90 c = 107.29 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2010-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.15 50 97.7 0.07 22.53 7.8 22362 21857 -3 31.38
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) 2.15 2.21 84.3 0.364 3.7 4.2 1607
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 deposition 2ys7 modified with CCP4 program CHAINSAW 2.15 43.47 22362 21807 1128 97.8 0.172 0.172 0.17 0.1742 0.215 0.2208 RANDOM 19.14
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] -0.05 -0.14 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.128 r_scangle_it 3.504 r_scbond_it 2.157 r_angle_refined_deg 1.351 r_mcangle_it 1.188 r_angle_other_deg 0.866 r_mcbond_it 0.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 6.128 r_scangle_it 3.504 r_scbond_it 2.157 r_angle_refined_deg 1.351 r_mcangle_it 1.188 r_angle_other_deg 0.866 r_mcbond_it 0.618 r_mcbond_other 0.154 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 10
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling