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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 7 298 15%PEG 1500, 10mM magnesium chloride and 5mM sodium tungstate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.526 α = 90 b = 56.339 β = 90 c = 93.77 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 210 mirrors 2005-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.9000 NSLS X12C
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 1.07 50 98 0.083 0.083 21.2 8 114002 114002 2 2 8.8
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 1.07 1.11 91.6 0.501 0.028 0.028 3.7 10529
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1.07 10 2 113636 113636 11375 98 0.1169 0.1169 0.1169 0.1228 0.1489 0.1251 RANDOM 18.4
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] 1.66 -0.71 -0.95
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 16 1751 2548
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.109 s_non_zero_chiral_vol 0.084 s_zero_chiral_vol 0.076 s_similar_adp_cmpnt 0.034 s_angle_d 0.031 s_from_restr_planes 0.0276 s_anti_bump_dis_restr 0.02 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 6
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CBASS data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing