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Crystal structure of human myo-inositol monophosphatase 2 (IMPA2) with phosphate ion (orthorhombic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HHM PDB ENTRY 2HHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.01M Potassium dihydrogen phosphate, 15% PEG 8000, 20% Glycerol, 2mM MgSO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.265 α = 90 b = 97.043 β = 90 c = 104.922 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 RIGAKU JUPITER 210 Two dimensional focusing mirror 2004-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
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 2.7 50 100 0.078 21.7 5.9 18870 -3 56.5
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) 2.7 2.8 100 0.438 4.1 6 1566
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 2HHM 2.7 48.52 18309 1738 97 0.212 0.212 0.2119 0.247 0.2451 RANDOM 53.7
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] 1.89 -1.87 -0.02
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 11.23 c_scbond_it 8.92 c_mcangle_it 7.3 c_mcbond_it 5.37 c_angle_deg 1.5 c_improper_angle_d 0.88 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 11.23 c_scbond_it 8.92 c_mcangle_it 7.3 c_mcbond_it 5.37 c_angle_deg 1.5 c_improper_angle_d 0.88 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3849 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing