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Crystal structure (Type-2) of SAICAR synthetase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U54 PDB ENTRY 3U54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDEROIL 4.6 293 0.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE TRIHYDRATE, 30% PEG MONOMETHYL ETHER, pH 4.6, MICROBATCH UNDEROIL, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.1 α = 90 b = 155.39 β = 90 c = 78.35 γ = 90
Symmetry Space Group C 2 2 21
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 MAR scanner 345 mm plate MIRRORS 2011-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 42.42 98.9 0.042 24.1 5.3 21450 21.5
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 1.9 2 97.5 0.191 8 5.2 3041
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 3U54 1.9 42.42 20332 1096 98.66 0.18601 0.18366 0.183 0.22924 0.2277 RANDOM 22.825
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] -0.1 0.54 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_3_deg 13.554 r_dihedral_angle_4_deg 10.713 r_scangle_it 5.044 r_dihedral_angle_1_deg 4.911 r_scbond_it 3.157 r_mcangle_it 1.947 r_mcbond_it 1.151 r_angle_refined_deg 0.992 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.998 r_dihedral_angle_3_deg 13.554 r_dihedral_angle_4_deg 10.713 r_scangle_it 5.044 r_dihedral_angle_1_deg 4.911 r_scbond_it 3.157 r_mcangle_it 1.947 r_mcbond_it 1.151 r_angle_refined_deg 0.992 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1806 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 14
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling