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Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Obtained from MAD data of a crystal of SE-MET substituted protein in space group P21 21 2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 0.12M Na Cl, 0.90M Tartrate_K Na, 0.084M Imidazole, 0.016M Imidazole Chloride , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.04 2.78 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.98 α = 90 b = 129.98 β = 90 c = 131.32 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 CCD ADSC QUANTUM 315 FLAT MIRROR 2002-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 2.3 29.41 98 0.059 14.5 3.9 28995 49.54
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 2.3 2.42 98.6 0.344 3.9 3.9 4221
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Obtained from MAD data of a crystal of SE-MET substituted protein in space group P21 21 2 2.3 29.41 27525 1470 97.55 0.20352 0.20035 0.26455 0.2634 RANDOM 32.35
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] 4.39 1.05 -5.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.468 r_dihedral_angle_3_deg 17.577 r_dihedral_angle_4_deg 16.642 r_scangle_it 8.73 r_dihedral_angle_1_deg 6.944 r_scbond_it 6.732 r_mcangle_it 3.433 r_mcbond_it 1.976 r_angle_refined_deg 1.608 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.468 r_dihedral_angle_3_deg 17.577 r_dihedral_angle_4_deg 16.642 r_scangle_it 8.73 r_dihedral_angle_1_deg 6.944 r_scbond_it 6.732 r_mcangle_it 3.433 r_mcbond_it 1.976 r_angle_refined_deg 1.608 r_nbtor_refined 0.312 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.165 r_metal_ion_refined 0.152 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4007 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 58
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELXD phasing autoSHARP phasing REFMAC refinement CCP4 data scaling MOLREP phasing