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Crystal Structure of Murraya koenigii Miraculin-Like Protein at 2.2 A resolution at pH 7.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IIR PDB ENTRY 3IIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 4M AMMONIUM ACETATE, 0.1M BIS-TRIS PROPANE, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.13 42.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.51 α = 90 b = 45.69 β = 95.02 c = 38.78 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate 2011-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER
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 2.24 50.56 96.3 0.09 10.3 3.3 8649 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.33 74.9 0.27 4.4 3.1
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 3IIR 2.24 50.56 8240 409 99.6 0.19548 0.19316 0.1924 0.24172 0.2431 RANDOM 16.55
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] -0.54 -0.59 0.63 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.916 r_dihedral_angle_4_deg 16.967 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 6.427 r_mcangle_it 1.558 r_angle_refined_deg 1.174 r_mcbond_it 0.84 r_scbond_it 0.582 r_chiral_restr 0.075 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.916 r_dihedral_angle_4_deg 16.967 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 6.427 r_mcangle_it 1.558 r_angle_refined_deg 1.174 r_mcbond_it 0.84 r_scbond_it 0.582 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1409 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing