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L-myo-inositol 1-phosphate synthase from Archaeoglobus fulgidus wild type
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, HANGING DROP 7.5 293 0.2 M calcium chloride, 14% PEG400, 15% PEG1500, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.47 α = 90 b = 89.5 β = 90 c = 104.62 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 293 IMAGE PLATE RIGAKU RAXIS IV Osmic Blue 2004-10-22 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 1.69 68.041 99 0.061 21.1 4.1 42214 42024 22.9
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 1.69 1.76 95 0.34 2 3 3897
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 1.7 68.04 40084 2123 98.11 0.20104 0.1988 0.1965 0.24345 0.2406 RANDOM 28.519
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] -0.41 2.32 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.75 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_4_deg 13.737 r_dihedral_angle_1_deg 5.748 r_scangle_it 3.465 r_scbond_it 2.394 r_angle_refined_deg 1.662 r_mcangle_it 1.303 r_mcbond_it 0.807 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.75 r_dihedral_angle_3_deg 15.214 r_dihedral_angle_4_deg 13.737 r_dihedral_angle_1_deg 5.748 r_scangle_it 3.465 r_scbond_it 2.394 r_angle_refined_deg 1.662 r_mcangle_it 1.303 r_mcbond_it 0.807 r_nbtor_refined 0.306 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.194 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 3084 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing