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The 3D structure of chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1THF PDB entry 1THF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 7 292 20% PEG 3350, 0.1M Bis-Tris propane pH 8.5, 0.2M NaF, pH 7.0, MICROBATCH UNDER OIL, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.71 66.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.38 α = 90 b = 96.38 β = 90 c = 153.988 γ = 120
Symmetry Space Group P 61 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++ Mirrors 2007-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.25 50 99.9 0.098 0.087 36.6 19.7 20784 20784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.33 100 0.435 0.392 6.8 18.9 2025
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1THF 2.25 50 19746 19657 1066 99.55 0.20716 0.2057 0.2033 0.23481 0.2308 RANDOM 33.665
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.467 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 14.81 r_dihedral_angle_1_deg 6.59 r_scangle_it 5.038 r_scbond_it 3.34 r_mcangle_it 2.016 r_angle_refined_deg 1.74 r_mcbond_it 1.29 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.467 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 14.81 r_dihedral_angle_1_deg 6.59 r_scangle_it 5.038 r_scbond_it 3.34 r_mcangle_it 2.016 r_angle_refined_deg 1.74 r_mcbond_it 1.29 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.116 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1940 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing