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Crystal structure of 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 5.6, 35 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.28 α = 90 b = 65.28 β = 90 c = 97.141 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 2016-08-24 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) R Merge I (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 56.53 99.4 0.112 0.99 4.27 7 52939 18.5
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 83.6 0.766
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 56.53 50243 2667 99.4 0.1693 0.167 0.1818 0.2177 0.2309 RANDOM 21.531
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 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.018 r_dihedral_angle_4_deg 16.56 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 5.986 r_angle_refined_deg 2.137 r_angle_other_deg 1.172 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.018 r_dihedral_angle_4_deg 16.56 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 5.986 r_angle_refined_deg 2.137 r_angle_other_deg 1.172 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 1286
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing