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Rat metallophosphodiesterase MPPED2 H67R Mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 Ammonium nitrate, PEG 3350, CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.622 α = 90 b = 69.848 β = 103.52 c = 47.182 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm monochromators, mirrors 2009-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.99996 ELETTRA 5.2R
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 1.26 50 99.9 0.059 16.9 4.1 84002 83943 -3 11.242
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 1.26 1.29 99.2 0.251 3.9 5512
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.26 20.75 84002 83935 8430 99.92 0.1542 0.1519 0.1615 0.1744 0.1841 RANDOM 16.8614
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] 0.27 -0.39 -0.1 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_4_deg 14.253 r_dihedral_angle_3_deg 10.556 r_dihedral_angle_1_deg 6.279 r_sphericity_free 5.16 r_sphericity_bonded 4.09 r_scangle_it 3.475 r_scbond_it 3.124 r_rigid_bond_restr 2.939 r_mcangle_it 2.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_4_deg 14.253 r_dihedral_angle_3_deg 10.556 r_dihedral_angle_1_deg 6.279 r_sphericity_free 5.16 r_sphericity_bonded 4.09 r_scangle_it 3.475 r_scbond_it 3.124 r_rigid_bond_restr 2.939 r_mcangle_it 2.045 r_mcbond_it 1.389 r_angle_refined_deg 1.323 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.301 r_nbd_refined 0.199 r_symmetry_metal_ion_refined 0.126 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.094 r_metal_ion_refined 0.092 r_symmetry_hbond_refined 0.061 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 10
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction