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Human hypoxanthine guanine phosphoribosyltranserfase in complex with (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)guanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M citrate, 10% isopropanol, 29% PEG 4000, 3.9mM (RS)- HPMPG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.122 α = 90 b = 72.59 β = 90 c = 51.282 γ = 90
Symmetry Space Group P 21 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 100 CCD RIGAKU SATURN 944 mirrors 2007-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 2.6 29.63 99.5 0.079 0.079 9.3 4.5 13343 13343
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) 2.6 2.69 99.4 0.179 0.179 4.5 4.3 1334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 1Z7G 2.6 29.63 12298 666 97.53 0.24984 0.24725 0.2545 0.2983 0.3046 RANDOM 45.26
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] -0.43 0.15 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_4_deg 24.593 r_dihedral_angle_3_deg 19.28 r_dihedral_angle_1_deg 8.287 r_mcangle_it 5.521 r_mcbond_it 3.771 r_scangle_it 2.889 r_scbond_it 1.749 r_angle_refined_deg 1.269 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_4_deg 24.593 r_dihedral_angle_3_deg 19.28 r_dihedral_angle_1_deg 8.287 r_mcangle_it 5.521 r_mcbond_it 3.771 r_scangle_it 2.889 r_scbond_it 1.749 r_angle_refined_deg 1.269 r_nbtor_refined 0.306 r_chiral_restr 0.234 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.157 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3283 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling