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The Structure of Ultra Stable Green Fluorescent Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 20 % w/v PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M Sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.182 α = 90 b = 137.182 β = 90 c = 147.647 γ = 120
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 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.9 49.22 99.4 0.089 0.097 0.999 17.8 11.2 41787
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 1.9 1.94 98.7 1.059 2.7 11.4
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 2B3P 1.9 49.22 39749 2035 99.23 0.14405 0.14232 0.1541 0.17639 0.1853 RANDOM 33.954
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] 0.47 0.24 0.47 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.378 r_dihedral_angle_3_deg 13.052 r_long_range_B_other 7.766 r_long_range_B_refined 7.765 r_dihedral_angle_1_deg 6.678 r_scangle_other 4.342 r_scbond_it 2.766 r_scbond_other 2.763 r_mcangle_it 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.378 r_dihedral_angle_3_deg 13.052 r_long_range_B_other 7.766 r_long_range_B_refined 7.765 r_dihedral_angle_1_deg 6.678 r_scangle_other 4.342 r_scbond_it 2.766 r_scbond_other 2.763 r_mcangle_it 2.165 r_mcangle_other 2.165 r_angle_refined_deg 1.572 r_mcbond_it 1.486 r_mcbond_other 1.484 r_angle_other_deg 0.754 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 3730 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing