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X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with beta-D-erythrofuranosyl- adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C2W PDB ENTRY 2C2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 32% PEG 1K 100 MM PHOSPHATE CITRATE PH4.2 200 MM LI2SO4, pH 4.00
Crystal Properties Matthews coefficient Solvent content 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.815 α = 90 b = 128.017 β = 90 c = 181.028 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 CCD ADSC CCD MIRRORS 2005-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 52.56 97.6 0.07 14.7 3.7 209563 2
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 2.11 97.1 0.38 3.1 3.7
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 2C2W 2 90.54 54334 2898 97 0.176 0.172 0.239 RANDOM 23.56
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] -0.08 -0.44 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.907 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 6.966 r_scangle_it 3.507 r_scbond_it 2.422 r_angle_refined_deg 1.408 r_mcangle_it 1.398 r_mcbond_it 0.881 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.907 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 6.966 r_scangle_it 3.507 r_scbond_it 2.422 r_angle_refined_deg 1.408 r_mcangle_it 1.398 r_mcbond_it 0.881 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 495 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing