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Crystal structure of full-length HypF in the phosphate- and nucleotide-bound form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 288 0.1M imidazole, 1.8M Na/K phosphate, 0.2M NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.983 α = 90 b = 232.983 β = 90 c = 65.665 γ = 120
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 MX225HE 2011-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 20 98 0.096 18.4 6.3 135176 135176 31.4
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 2.03 96.8 0.497 4.2 5.2 6623
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 MOLECULAR REPLACEMENT THROUGHOUT 2 20 126835 6631 97 0.21076 0.20935 0.2224 0.23758 0.2501 RANDOM 46.815
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] -0.95 -0.47 -0.95 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.966 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_4_deg 14.536 r_dihedral_angle_1_deg 5.685 r_scangle_it 2.918 r_scbond_it 1.747 r_angle_refined_deg 1.255 r_mcangle_it 1.021 r_mcbond_it 0.524 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.966 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_4_deg 14.536 r_dihedral_angle_1_deg 5.685 r_scangle_it 2.918 r_scbond_it 1.747 r_angle_refined_deg 1.255 r_mcangle_it 1.021 r_mcbond_it 0.524 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11094 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 176
Software Software Software Name Purpose BSS data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling