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Structure of analogue of superfolded GFP
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 291 PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, Bicine/Trizma 0.1 M pH 8.5, Morpheus III Alkaloids 0.8% w/v, Morpheus Alcohols 0.12 M
Crystal Properties Matthews coefficient Solvent content 1.93 36.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.516 α = 90 b = 37.721 β = 106.376 c = 91.795 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 PIXEL DECTRIS PILATUS3 2M 2023-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.84 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.537 88.071 93.1 0.11 0.99 5.1 3.3 59575
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.537 1.595 1.35 0.34
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.537 88.071 59575 2978 92.414 0.187 0.1858 0.1968 0.2145 0.2232 18.863
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] -0.578 -0.501 0.539 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.34 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_4_deg 10.163 r_dihedral_angle_1_deg 7.302 r_lrange_it 5.93 r_lrange_other 5.923 r_scangle_it 4.919 r_scangle_other 4.919 r_scbond_it 3.128 r_scbond_other 3.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.34 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_4_deg 10.163 r_dihedral_angle_1_deg 7.302 r_lrange_it 5.93 r_lrange_other 5.923 r_scangle_it 4.919 r_scangle_other 4.919 r_scbond_it 3.128 r_scbond_other 3.127 r_mcangle_it 2.407 r_mcangle_other 2.407 r_angle_refined_deg 1.789 r_mcbond_it 1.672 r_mcbond_other 1.669 r_angle_other_deg 1.406 r_nbd_refined 0.342 r_xyhbond_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.216 r_nbd_other 0.2 r_symmetry_nbd_refined 0.178 r_nbtor_refined 0.163 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3149 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 477
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing