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L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus mutant K278A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1I PDB ENTRY 1U1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M calcium chloride, 14% PEG400, 15% PEG1500, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.26 α = 90 b = 89.94 β = 90 c = 104.865 γ = 90
Symmetry Space Group I 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 RIGAKU RAXIS IV++ Osmic Blue 2005-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 68.2 97.9 0.088 7.7 2.6 26722 26097 21.6
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 2.07 96.8 0.384 2.1 1.8 21459
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 ENTRY 1U1I 2 68.2 24770 1320 97.6 0.21836 0.21504 0.2229 0.28198 0.2894 RANDOM 29.151
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] -0.61 2.12 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_3_deg 16.797 r_dihedral_angle_4_deg 13.503 r_dihedral_angle_1_deg 6.301 r_scangle_it 3.287 r_scbond_it 2.369 r_angle_refined_deg 1.927 r_mcangle_it 1.364 r_mcbond_it 0.793 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_3_deg 16.797 r_dihedral_angle_4_deg 13.503 r_dihedral_angle_1_deg 6.301 r_scangle_it 3.287 r_scbond_it 2.369 r_angle_refined_deg 1.927 r_mcangle_it 1.364 r_mcbond_it 0.793 r_nbtor_refined 0.32 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.232 r_symmetry_hbond_refined 0.231 r_symmetry_vdw_refined 0.212 r_chiral_restr 0.115 r_bond_refined_d 0.018 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 3080 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing