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Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl transfer Reaction observed on cocrystallization with Glucose 1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMeth MAD model of the same protein to 1.7 angstrom
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 291 16% PEG 3350, 0.1M Ammonium Fluoride, 4mM b-D-Glucose-1-phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.87 26.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.939 α = 90 b = 54.297 β = 90 c = 104.68 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 93 CCD ADSC QUANTUM 4 mirrors 2002-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.2 100 86.9 0.043 0.045 32.7 10.6 56998 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) 1.2 1.22 54.4 0.113 0.08 15.7
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 (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 THROUGHOUT SeMeth MAD model of the same protein to 1.7
angstrom 1.2 10 50842 49967 5756 76.8 0.1408 0.1408 0.147 0.1792 0.2004 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 5 2205
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.077 s_non_zero_chiral_vol 0.069 s_similar_adp_cmpnt 0.037 s_angle_d 0.032 s_anti_bump_dis_restr 0.028 s_from_restr_planes 0.0274 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 21
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling SHELX phasing