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L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus mutant K367A
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 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.07 α = 90 b = 89.28 β = 90 c = 104.97 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 2005-02-16 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 1.9 68.041 96.7 0.04 14.6 2.9 30995 29996 22
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 1.89 1.96 94.6 0.214 3.9 2.3 2371
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 1.9 68.04 28479 1512 96.81 0.17733 0.17462 0.1736 0.22917 0.2286 RANDOM 24.886
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] 0.04 2.38 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.8 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 14.728 r_dihedral_angle_1_deg 5.61 r_scangle_it 3.141 r_scbond_it 2.115 r_angle_refined_deg 1.533 r_mcangle_it 1.16 r_mcbond_it 0.66 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.8 r_dihedral_angle_3_deg 15.249 r_dihedral_angle_4_deg 14.728 r_dihedral_angle_1_deg 5.61 r_scangle_it 3.141 r_scbond_it 2.115 r_angle_refined_deg 1.533 r_mcangle_it 1.16 r_mcbond_it 0.66 r_nbtor_refined 0.305 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 234 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing