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Crystal structure of IMPase/NADP phosphatase complexed with NADP and Ca2+
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 6.5 298 0.2M CACL2 2H2O, 0.1M BIS-TRIS PH 6.5, 22%(W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.089 α = 90 b = 78.88 β = 90 c = 112.409 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-03-05 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 2.2 64.569 99.9 0.121 0.13 0.048 16.4 7.2 33204 33204
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 2.2 2.32 99.9 0.48 0.48 0.193 1.6 7.2 4778
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 2.2 19.59 31471 1680 99.78 0.1635 0.1612 0.1724 0.2071 0.2177 RANDOM 23.678
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] 0.55 0.4 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.424 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_4_deg 8.466 r_dihedral_angle_1_deg 6.949 r_mcangle_it 2.13 r_angle_refined_deg 2.111 r_mcbond_it 1.345 r_mcbond_other 1.343 r_angle_other_deg 1.296 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.424 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_4_deg 8.466 r_dihedral_angle_1_deg 6.949 r_mcangle_it 2.13 r_angle_refined_deg 2.111 r_mcbond_it 1.345 r_mcbond_other 1.343 r_angle_other_deg 1.296 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4154 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 164
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing