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Crystal structure of dual specific IMPase/NADP phosphatase bound with D-inositol-1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.2M CACL2 2H20, 0.1M HEPES PH 7.0, 15% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.567 α = 90 b = 67.835 β = 90 c = 137.297 γ = 90
Symmetry Space Group P 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.498 68.648 99.8 0.106 0.114 0.042 18.9 7.2 20273 20273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63 99.9 0.497 0.497 0.199 1.6 7.2 2915
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 3QMF 2.5 68.4 19202 1035 99.68 0.1753 0.1722 0.1816 0.2329 0.2361 RANDOM 31.816
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] -0.88 0.86 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_3_deg 16.24 r_dihedral_angle_4_deg 15.179 r_dihedral_angle_1_deg 7.982 r_mcangle_it 2.596 r_angle_refined_deg 1.832 r_mcbond_it 1.556 r_mcbond_other 1.554 r_angle_other_deg 1.131 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_3_deg 16.24 r_dihedral_angle_4_deg 15.179 r_dihedral_angle_1_deg 7.982 r_mcangle_it 2.596 r_angle_refined_deg 1.832 r_mcbond_it 1.556 r_mcbond_other 1.554 r_angle_other_deg 1.131 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4084 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 94
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing