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Miraculin-like protein from Vitis vinifera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.1 M MES buffer (pH 6.5), 12% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.04 α = 90 b = 59.6 β = 90 c = 74.78 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 ADSC QUANTUM 315r 2016-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 35.93 100 11.9 6.1 50318
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 3ZC8 1.3 35.93 47798 2455 99.98 0.17492 0.17423 0.1834 0.18824 0.1953 RANDOM 12.658
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 9.83 r_dihedral_angle_1_deg 6.186 r_long_range_B_refined 4.67 r_long_range_B_other 4.089 r_scangle_other 1.457 r_mcangle_it 1.409 r_mcangle_other 1.409 r_angle_refined_deg 1.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.727 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 9.83 r_dihedral_angle_1_deg 6.186 r_long_range_B_refined 4.67 r_long_range_B_other 4.089 r_scangle_other 1.457 r_mcangle_it 1.409 r_mcangle_other 1.409 r_angle_refined_deg 1.355 r_scbond_it 0.9 r_scbond_other 0.898 r_angle_other_deg 0.863 r_mcbond_it 0.807 r_mcbond_other 0.802 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1397 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing