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CRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANOSINE-5'-MONOPHOSPHATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 ammonium sulfate, sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.3 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.625 α = 90 b = 50.625 β = 90 c = 155.327 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAC Science DIP-2000 MIRROR 1996-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 15 94.4 0.095 14.6 4.6 15836 15836 33.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.93 86.9 0.378 1.8455 3.8 716
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION REFINEMENT OF THE MODEL FREE R 1GKY 1.9 15 2 4 14174 11611 1575 84.7 0.1701 0.1701 0.1654 0.257 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 1688
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.085 s_non_zero_chiral_vol 0.044 s_zero_chiral_vol 0.035 s_angle_d 0.033 s_from_restr_planes 0.021 s_anti_bump_dis_restr 0.013 s_bond_d 0.01 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1446 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 34
Software Software Software Name Purpose X-PLOR model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing