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Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XRG PDB ENTRY 2XRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100 NL PROTEIN SOLUTION WITH 100 NL 10% PROPANOL, 0.1 M IMIDAZOLE AT PH 8.0 AND 3% 1,4-DIOXANE
Crystal Properties Matthews coefficient Solvent content 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.385 α = 90 b = 105.412 β = 90 c = 245.258 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2012-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 3 48.47 99.7 0.05 17.1 3.7 51597 1 110
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 3.16 99.8 0.64 2.1 3.8
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 PDB ENTRY 2XRG 3 48.47 51597 2763 99.73 0.202 0.2002 0.2065 0.2335 0.2373 RANDOM 116.185
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] 3.484 7.41 -10.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_4_deg 15.861 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.236 r_scangle_it 6.145 r_scbond_it 4.46 r_mcangle_it 2.887 r_mcbond_it 1.734 r_angle_refined_deg 1.271 r_angle_other_deg 0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_4_deg 15.861 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 6.236 r_scangle_it 6.145 r_scbond_it 4.46 r_mcangle_it 2.887 r_mcbond_it 1.734 r_angle_refined_deg 1.271 r_angle_other_deg 0.868 r_mcbond_other 0.355 r_nbd_refined 0.21 r_nbd_other 0.183 r_nbtor_refined 0.183 r_symmetry_vdw_other 0.183 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.108 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12573 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing