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Crystal structure of cytidine deaminase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM HEPES and 4.3 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.705 α = 90 b = 75.338 β = 90 c = 55.116 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAC Science DIP-3000 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.437 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.99 22.27 97 0.086 0.086 10 2.3 20845 9374 2 2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2fr5 1.99 18.24 9374 8621 433 96.99 0.19264 0.19017 0.24015 0.2236 RANDOM 17.537
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 20.873 r_dihedral_angle_4_deg 17.69 r_dihedral_angle_1_deg 5.942 r_scangle_it 4.037 r_scbond_it 2.855 r_angle_refined_deg 2.161 r_mcangle_it 1.658 r_mcbond_it 0.974 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.68 r_dihedral_angle_3_deg 20.873 r_dihedral_angle_4_deg 17.69 r_dihedral_angle_1_deg 5.942 r_scangle_it 4.037 r_scbond_it 2.855 r_angle_refined_deg 2.161 r_mcangle_it 1.658 r_mcbond_it 0.974 r_nbtor_refined 0.312 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.21 r_chiral_restr 0.191 r_xyhbond_nbd_refined 0.171 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 893 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 1
Software Software Software Name Purpose HKL-3000 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling