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Crystal structure of acivicin-bound GATase subunit of Methanocaldococcus jannaschii GMP synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.6 277 100 mM Sodium acetate, pH 4.6, 35 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.35 α = 90 b = 65.35 β = 90 c = 97.371 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 277 IMAGE PLATE MAR scanner 345 mm plate 2016-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.67 56.59 99.5 0.994 1.84 6.4 53661 21.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.76 0.858
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 1WL8 1.67 56.59 50917 2703 99.55 0.1982 0.1965 0.2097 0.2336 0.2457 RANDOM 24.476
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] 0.24 0.12 0.24 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 13.145 r_dihedral_angle_1_deg 5.891 r_angle_refined_deg 2.384 r_angle_other_deg 1.274 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 17.094 r_dihedral_angle_3_deg 13.145 r_dihedral_angle_1_deg 5.891 r_angle_refined_deg 2.384 r_angle_other_deg 1.274 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing