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Crystal Structure of Miraculin like protein from seeds of Murraya koenigii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVA PDB Entry 1AVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 6% PEG 8000, 0.1mM Tris-Cl pH 8.0, 0.08M Sodium Chloride, 0.08M Calcium Chloride, 8% Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.795 α = 90 b = 75.795 β = 90 c = 150.848 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate 2006-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 25 96.1 0.146 0.146 4.7 5.6 10300 58581 51.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 2.95 99.9 0.422 0.422 4.7 3.8 540
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1AVA 2.9 10 2 9300 473 97.56 0.21985 0.21618 0.2248 0.29452 0.299 RANDOM 27.074
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_3_deg 20.025 r_dihedral_angle_4_deg 17.008 r_dihedral_angle_1_deg 7.794 r_angle_refined_deg 1.668 r_scangle_it 1.534 r_scbond_it 0.932 r_mcangle_it 0.858 r_mcbond_it 0.527 r_symmetry_vdw_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_3_deg 20.025 r_dihedral_angle_4_deg 17.008 r_dihedral_angle_1_deg 7.794 r_angle_refined_deg 1.668 r_scangle_it 1.534 r_scbond_it 0.932 r_mcangle_it 0.858 r_mcbond_it 0.527 r_symmetry_vdw_refined 0.336 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.302 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling