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Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma phagocytophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 EMERALD JCSG SCREEN CONDITION A2. 100 MM CITRATE PH 5.0, 20% PEG 3000. PROTEIN CONCENTRATION 54 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.87 57.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.45 α = 90 b = 125.247 β = 95.44 c = 138.537 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 RAYONIX MX-225 2009-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97953 CLSI 08ID-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 2.2 50 85.4 0.081 9.7 3.4 45778
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 2.2 2.24 81.9 0.449 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1ZLY 2.2 50 45777 2324 0.212 0.21 0.2129 0.263 0.2641 RANDOM 14.24
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] -1.65 0.29 -1.35 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.084 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_4_deg 16.149 r_dihedral_angle_1_deg 5.915 r_scangle_it 2.844 r_scbond_it 1.758 r_angle_refined_deg 1.366 r_mcangle_it 1.154 r_angle_other_deg 0.901 r_mcbond_it 0.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.084 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_4_deg 16.149 r_dihedral_angle_1_deg 5.915 r_scangle_it 2.844 r_scbond_it 1.758 r_angle_refined_deg 1.366 r_mcangle_it 1.154 r_angle_other_deg 0.901 r_mcbond_it 0.623 r_mcbond_other 0.134 r_chiral_restr 0.079 r_bond_refined_d 0.013 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 6231 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 24
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling