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Crystal structure of phosphoribosylaminoimidazole-succinocarboxamide synthase from Ehrlichia chaffeensis at 1.8A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YWV pdb entry 2ywv modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 EBS SCREEN JCSG+ G1: 100MM HEPES PH 7.0, 30% JEFFAMINE ED-2001; EHCHA.00530.A AT 50MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.96 α = 90 b = 61.92 β = 117.99 c = 68.2 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 944 Rigaku VariMax HF 2009-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 20 94.1 0.056 21.59 4.7 26063 24514 -3 21.61
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 1.8 1.85 82.4 0.472 2.8 2.8 1557
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 2ywv modified with CCP4 program CHAINSAW 1.8 20 24514 24514 1249 94.4 0.155 0.155 0.153 0.1609 0.19 0.1974 RANDOM 8.83
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] -0.57 -0.64 0.25 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.084 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.9 r_scbond_it 2.343 r_mcangle_it 1.601 r_angle_refined_deg 1.486 r_mcbond_it 0.891 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.084 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 13.102 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.9 r_scbond_it 2.343 r_mcangle_it 1.601 r_angle_refined_deg 1.486 r_mcbond_it 0.891 r_angle_other_deg 0.872 r_mcbond_other 0.254 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1921 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 42
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling