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Crystal structure of HEP-CMP-bound form of cytidylyltransferase (CyTase) domain of Fom1 from Streptomyces wedmorensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES, 4.3 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.29 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.909 α = 90 b = 71.909 β = 90 c = 109.507 γ = 120
Symmetry Space Group P 65 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 95 CCD ADSC QUANTUM 270 2013-11-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97908, 0.97927, 0.96404 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.93 50 99.9 63.1 20.9 13233
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.93 30.05 12523 649 99.92 0.19307 0.19111 0.1992 0.23376 0.2399 RANDOM 34.472
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.103 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 14.154 r_long_range_B_refined 6.316 r_dihedral_angle_1_deg 6.288 r_long_range_B_other 6.227 r_scangle_other 5.001 r_scbond_it 3.319 r_scbond_other 3.318 r_mcangle_it 3.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.103 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 14.154 r_long_range_B_refined 6.316 r_dihedral_angle_1_deg 6.288 r_long_range_B_other 6.227 r_scangle_other 5.001 r_scbond_it 3.319 r_scbond_other 3.318 r_mcangle_it 3.262 r_mcangle_other 3.261 r_mcbond_it 2.401 r_mcbond_other 2.379 r_angle_refined_deg 1.643 r_angle_other_deg 1.071 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 994 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing