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Crystal structure (Type-1) of SAICAR synthetase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YZL PDB ENTRY 2YZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDEROIL 7.5 293 0.05M cadmium sulfate hydrate, 0.1M HEPES buffer, 1.0M sodium acetate trihydrate, 40%(w/v) 1,4-butanediol, pH 7.5, MICROBATCH UNDEROIL, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.42 α = 90 b = 95.42 β = 90 c = 148.631 γ = 120
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 2010-08-15 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 2.35 55.26 100 0.082 13.2 4.1 21057 33.1
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 2.35 2.48 100 0.4 3.1 4
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 2YZL 2.35 55.26 19974 1081 99.99 0.23746 0.23483 0.2323 0.28632 0.2834 RANDOM 24.812
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.359 r_dihedral_angle_3_deg 17.8 r_dihedral_angle_4_deg 17.61 r_scangle_it 8.186 r_scbond_it 6.237 r_dihedral_angle_1_deg 5.837 r_mcangle_it 3.993 r_mcbond_it 3.069 r_angle_refined_deg 1.285 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.359 r_dihedral_angle_3_deg 17.8 r_dihedral_angle_4_deg 17.61 r_scangle_it 8.186 r_scbond_it 6.237 r_dihedral_angle_1_deg 5.837 r_mcangle_it 3.993 r_mcbond_it 3.069 r_angle_refined_deg 1.285 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3529 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 42
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling