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X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-5'deoxy-fluoroadenosine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQP PDB ENTRY 1RQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 32%PEG 1K, 100MM PHOSPHATECITRATE PH4.2, 200MM LI2SO4, pH 4.00
Crystal Properties Matthews coefficient Solvent content 2.37 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.153 α = 90 b = 129.669 β = 90 c = 183.165 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 IMAGE PLATE RAXIS OSMIC MIRRORS 2005-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.5 37.69 87 0.14 7.3 2.9 27454 3
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 2.5 2.64 88 0.32 3.4 3.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RQP 2.5 37 26074 1344 86.3 0.193 0.189 0.267 RANDOM 10.51
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] 0.99 -1.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_3_deg 17.246 r_dihedral_angle_1_deg 7.216 r_scangle_it 1.886 r_angle_refined_deg 1.408 r_scbond_it 1.191 r_mcangle_it 0.774 r_mcbond_it 0.442 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_3_deg 17.246 r_dihedral_angle_1_deg 7.216 r_scangle_it 1.886 r_angle_refined_deg 1.408 r_scbond_it 1.191 r_mcangle_it 0.774 r_mcbond_it 0.442 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.042 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6660 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing