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Crystal structure of Nicotinate-nucleotide pyrophosphorylase from Ehrlichia chaffeensis at 2.05A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNN pdb deposition 3GNN modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 MD PACT SCREEN E6: 20% PEG 3350, 200MM NA-FORMATE; EHCHA.01074.A AT 29MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.53 α = 113.01 b = 77.32 β = 91.82 c = 78.32 γ = 111.68
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 210r 2009-11-07 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 2.05 50 96.6 0.087 10.27 2.3 74747 72223 -3 24.47
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 2.05 2.1 95.4 0.42 2.4 2.3 5510
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 3GNN modified with CCP4 program CHAINSAW 2.05 50 74747 72216 3640 96.8 0.177 0.177 0.174 0.1755 0.226 0.2247 RANDOM 9.69
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] 0.28 -0.2 -0.05 -0.43 -0.26 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_dihedral_angle_4_deg 19.633 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.009 r_scangle_it 3.503 r_scbond_it 2.193 r_angle_refined_deg 1.454 r_mcangle_it 1.342 r_angle_other_deg 0.964 r_mcbond_it 0.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_dihedral_angle_4_deg 19.633 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 6.009 r_scangle_it 3.503 r_scbond_it 2.193 r_angle_refined_deg 1.454 r_mcangle_it 1.342 r_angle_other_deg 0.964 r_mcbond_it 0.732 r_mcbond_other 0.186 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 8303 Nucleic Acid Atoms Solvent Atoms 853 Heterogen Atoms 28
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling