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The PAPase Hal2p complexed with magnesium ions and reaction products: AMP and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QGX PDB ENTRY 1QGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30 % PEG5000 MME, 0.1 M sodium acetate, 5 mM beta-mercaptoethanol, 0.1 M MES (Crystals were soaked in mother liquor containing 1 M magnesium chloride for 1 hour), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.693 α = 90 b = 45.075 β = 110.96 c = 71.794 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU RAXIS 1999-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 67.42 99.5 25897 25897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.949 99.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QGX 1.9 67.42 25847 25847 1306 99.43 0.15845 0.1559 0.1655 0.20348 0.2085 RANDOM 19.369
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] -1.74 -0.42 1.47 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.566 r_dihedral_angle_1_deg 6.346 r_scangle_it 5.933 r_scbond_it 3.982 r_mcangle_it 2.656 r_angle_refined_deg 1.739 r_mcbond_it 1.711 r_angle_other_deg 0.83 r_symmetry_hbond_refined 0.349 r_symmetry_vdw_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.566 r_dihedral_angle_1_deg 6.346 r_scangle_it 5.933 r_scbond_it 3.982 r_mcangle_it 2.656 r_angle_refined_deg 1.739 r_mcbond_it 1.711 r_angle_other_deg 0.83 r_symmetry_hbond_refined 0.349 r_symmetry_vdw_refined 0.247 r_symmetry_vdw_other 0.244 r_nbd_refined 0.235 r_nbd_other 0.219 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_metal_ion_refined 0.01 r_gen_planes_refined 0.006 r_xyhbond_nbd_other 0.006 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2727 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 35
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement CCP4 data scaling