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Crystal structure of family II Inorganic pyrophosphatase in complex with PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 100mM HEPES/K+ (pH 7.5), 2.3-2.5M ammonium sulphate, 3-4% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.78 67.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.011 α = 90 b = 115.867 β = 90 c = 147.874 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 4 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 20 99.9 0.052 14.89 4.2 104553 104553 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 100 0.452 2.76 3.2 16261
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WPM 1.75 19.84 99323 99323 5228 100 0.16683 0.16582 0.18595 0.2942 RANDOM 43.744
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] -0.74 1.39 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.399 r_dihedral_angle_3_deg 14.627 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 5.787 r_scangle_it 4.566 r_mcangle_it 3.179 r_scbond_it 3.007 r_mcbond_it 2.366 r_angle_refined_deg 1.519 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.399 r_dihedral_angle_3_deg 14.627 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_1_deg 5.787 r_scangle_it 4.566 r_mcangle_it 3.179 r_scbond_it 3.007 r_mcbond_it 2.366 r_angle_refined_deg 1.519 r_nbtor_refined 0.308 r_nbd_refined 0.18 r_symmetry_hbond_refined 0.12 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.116 r_xyhbond_nbd_refined 0.114 r_metal_ion_refined 0.075 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_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 4744 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data scaling CNS phasing