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Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F3K PDB 3F3K molecule A protein atoms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 0.1M Hepes 7.5, 10%Iso-propnal, 22%PEG4K, 4%Glycerol, 0.03 mg/ml trypsin, soaking 10min in well solution w/10mM sedoheptulose. Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.559 α = 90.04 b = 74.945 β = 89.92 c = 83.615 γ = 77.22
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 RIGAKU SATURN A200 mirrors 2010-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.2 50 82.6 0.08 9.88 1.6 69828 57671 -3 25.5
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 2.24 36.9 0.112 3.02 1.3 1286
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 3F3K molecule A protein atoms 2.4 27.5 46894 2567 91.3 0.23007 0.22842 0.2281 0.25996 0.2598 RANDOM 23.929
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 0.02 0.01 -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 16.248 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_1_deg 6.149 r_scangle_it 4.735 r_scbond_it 2.76 r_mcangle_it 1.566 r_angle_refined_deg 1.355 r_mcbond_it 0.74 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.255 r_dihedral_angle_4_deg 16.248 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_1_deg 6.149 r_scangle_it 4.735 r_scbond_it 2.76 r_mcangle_it 1.566 r_angle_refined_deg 1.355 r_mcbond_it 0.74 r_nbtor_refined 0.301 r_metal_ion_refined 0.254 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.091 r_bond_refined_d 0.012 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_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 8392 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 135
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling