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Rat metallophosphodiesterase MPPED2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 MnCl2, PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.887 α = 90 b = 69.752 β = 103.14 c = 46.984 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 2009-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.97626 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 1.42 50 99 0.08 11.2 4 58321 57595 -3 16.093
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 1.42 1.45 97.3 0.491 3.8 3770
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 1.42 47.67 58321 57591 5810 98.72 0.1627 0.16 0.16 0.1871 0.1888 RANDOM 18.2092
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] 0.31 -0.34 0.29 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_3_deg 11.452 r_dihedral_angle_4_deg 8.95 r_dihedral_angle_1_deg 6.277 r_sphericity_free 4.559 r_scangle_it 3.175 r_sphericity_bonded 2.809 r_scbond_it 2.538 r_rigid_bond_restr 1.952 r_mcangle_it 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_3_deg 11.452 r_dihedral_angle_4_deg 8.95 r_dihedral_angle_1_deg 6.277 r_sphericity_free 4.559 r_scangle_it 3.175 r_sphericity_bonded 2.809 r_scbond_it 2.538 r_rigid_bond_restr 1.952 r_mcangle_it 1.751 r_angle_refined_deg 1.327 r_mcbond_it 1.159 r_nbtor_refined 0.318 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.096 r_metal_ion_refined 0.018 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2218 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 38
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction