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CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 PEG 4000, magnesium chloride, Tris-HCl, glycerol, acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal Properties Matthews coefficient Solvent content 2.13 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.053 α = 90 b = 61.857 β = 90 c = 67.106 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 IMAGE PLATE MARRESEARCH MIRROR 1999-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.85 40 89.5 0.154 5.9 3.1 14188 12732 0.025 0.05 17.4
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) 1.85 1.92 77.6 0.338 2.056 2.8 1384
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 1EQO 1.85 40 2 4 12025 9368 614 85.4 0.1854 0.2029 0.242 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 1478
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.081 s_non_zero_chiral_vol 0.032 s_zero_chiral_vol 0.028 s_from_restr_planes 0.026 s_angle_d 0.021 s_anti_bump_dis_restr 0.012 s_bond_d 0.006 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1267 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 50
Software Software Software Name Purpose AMoRE phasing SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling