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The PAPase Hal2p complexed with calcium and magnesium ions and reaction substrate: PAP
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 0.5 M calcium chloride for 5 hours.) , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.875 α = 90 b = 44.968 β = 110.72 c = 72.11 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 CCD ADSC QUANTUM 4 1999-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.8700 SRS PX9.6
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 1.3 50.31 90.3 0.08 16.4 2.9 73179 73179
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) 1.3 1.334 77.1 0.45 2.1 2.6
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 1.3 50 73179 73179 3654 90.28 0.13445 0.13261 0.1361 0.1693 0.1732 RANDOM 12.132
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] -0.04 0.27 0.22 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.123 r_sphericity_free 6.221 r_dihedral_angle_1_deg 6.181 r_scangle_it 6.143 r_sphericity_bonded 5.36 r_scbond_it 4.396 r_mcangle_it 3.214 r_rigid_bond_restr 2.631 r_mcbond_it 2.399 r_angle_refined_deg 1.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.123 r_sphericity_free 6.221 r_dihedral_angle_1_deg 6.181 r_scangle_it 6.143 r_sphericity_bonded 5.36 r_scbond_it 4.396 r_mcangle_it 3.214 r_rigid_bond_restr 2.631 r_mcbond_it 2.399 r_angle_refined_deg 1.723 r_angle_other_deg 1.253 r_nbtor_other 0.383 r_xyhbond_nbd_other 0.296 r_symmetry_vdw_other 0.274 r_nbd_refined 0.269 r_xyhbond_nbd_refined 0.267 r_symmetry_vdw_refined 0.259 r_symmetry_hbond_refined 0.254 r_nbd_other 0.225 r_chiral_restr 0.113 r_metal_ion_refined 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2719 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 33
Software Software Software Name Purpose ADSC data collection SCALA data scaling REFMAC refinement CCP4 data scaling