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Green fluorescent protein from Aequorea macrodactyla - amacGFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 amacGFP (12 mg/mL in 20 mM Tris-HCl buffer, pH 7.5) was crystallized at 21 C in 8% PEG 6K, 3% glycerol, 0.1 M sodium acetate, pH 5.0 supplemented with 5.0% Jeffamine M-600 pH 7.0 according to the Hampton Research Additive Screen protocol
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.089 α = 90 b = 47.488 β = 102.01 c = 69.294 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON III 2020-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.81 22.6 99.8 0.996 9.36 7.59 19894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.91 0.624
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 2AWK 1.81 22.6 18907 955 99.73 0.1838 0.1817 0.193 0.2275 0.2393 RANDOM 18.431
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] -0.01 0.26 0.25 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.289 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_4_deg 11.596 r_dihedral_angle_1_deg 7.632 r_mcangle_it 2.356 r_angle_refined_deg 1.65 r_mcbond_it 1.556 r_mcbond_other 1.551 r_angle_other_deg 1.315 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.289 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_4_deg 11.596 r_dihedral_angle_1_deg 7.632 r_mcangle_it 2.356 r_angle_refined_deg 1.65 r_mcbond_it 1.556 r_mcbond_other 1.551 r_angle_other_deg 1.315 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1836 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 555
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PROTEUM PLUS data scaling PDB_EXTRACT data extraction PROTEUM PLUS data reduction