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Crystal structure of Zn(II)-bound YjiA GTPase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NIJ PDB ENTRY 1NIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 1.5 uL of 13.2 mg/mL YjiA in 0.1 M NaCl, 25 mM HEPES, pH 7.6, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.55 M ammonium sulfate, 0.1 M , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 39.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.295 α = 90 b = 68.869 β = 104.09 c = 77.829 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2007-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.1808 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.57 30 97 0.079 18.3 3.8 35529 35529 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.61 84.6 0.412 3.3 3.6 1535
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1NIJ 2.57 29.126 1.36 35283 35283 940 97.46 0.2221 0.2199 0.2232 0.2623 0.2658 random 71.69
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.79 f_angle_d 0.56 f_chiral_restr 0.039 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4821 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 15
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling