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The Complex Structure of Mutant Phytase with IHS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.01 M NiCl2, 0.1 M HEPES, 20% PEG 3350 and 2% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.796 α = 90 b = 47.5 β = 100.51 c = 65.632 γ = 90
Symmetry Space Group P 1 21 1
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 2014-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
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 2.07 25 99.7 0.129 10.9 3.4 23694
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 1DKQ 2.07 25 22501 1182 99.6 0.17419 0.17181 0.181 0.21818 0.225 RANDOM 19.096
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] 1.62 0.23 -1.12 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 17.697 r_dihedral_angle_3_deg 17.375 r_dihedral_angle_1_deg 6.112 r_long_range_B_refined 5.41 r_long_range_B_other 5.242 r_scangle_other 3.052 r_scbond_it 2.046 r_scbond_other 2.026 r_mcangle_other 1.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 17.697 r_dihedral_angle_3_deg 17.375 r_dihedral_angle_1_deg 6.112 r_long_range_B_refined 5.41 r_long_range_B_other 5.242 r_scangle_other 3.052 r_scbond_it 2.046 r_scbond_other 2.026 r_mcangle_other 1.818 r_mcangle_it 1.817 r_angle_refined_deg 1.792 r_mcbond_it 1.142 r_mcbond_other 1.138 r_angle_other_deg 0.925 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement