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X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 10 mM MgCl2, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH=5.5) and 25% PEG 3350. Crystals were soaked with 2 mM sodium orthovanadate for 2 hours before data collection., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.533 α = 90 b = 56.356 β = 90 c = 94.026 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 4 mirrors 2005-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 0.9000 NSLS X12B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1 50 95.5 0.122 0.122 15 9.3 136055 136055 2 2 6.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.04 71.4 0.423 0.02 2 2.8 10056
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 AB INITIO FREE R 1YMQ 1 10 135801 135801 13574 88.7 0.1227 0.1227 0.1227 0.1306 0.1483 0.1296 RANDOM 17.6
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] 1.85 -0.86 -0.99
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 16 1899.5 2494
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.115 s_non_zero_chiral_vol 0.091 s_zero_chiral_vol 0.087 s_similar_adp_cmpnt 0.035 s_angle_d 0.034 s_from_restr_planes 0.0282 s_anti_bump_dis_restr 0.022 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2025 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 5
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CBASS data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing