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Monoclinic crystal structure of green fluorescent protein nowGFP at pH 4.8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 16mM KH2PO4 pH 4.8, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.547 α = 90 b = 51.039 β = 99.58 c = 55.515 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 CCD ADSC QUANTUM 270 2022-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.45 30 99.9 0.072 0.077 0.029 1 37.3 7.3 54859
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 100 0.688 0.742 0.275 0.827 2.5 7.2
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 (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 FREE R-VALUE 1.45 29.62 51316 2809 99.91 0.12869 0.12701 0.1358 0.15823 0.1652 RANDOM 23.705
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] -0.89 0.73 -3.5 3.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.579 r_mcangle_it 19.087 r_mcangle_other 19.081 r_rigid_bond_restr 18.446 r_long_range_B_other 15.367 r_mcbond_other 15.327 r_mcbond_it 15.323 r_long_range_B_refined 15.247 r_scangle_other 13.844 r_dihedral_angle_3_deg 12.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.579 r_mcangle_it 19.087 r_mcangle_other 19.081 r_rigid_bond_restr 18.446 r_long_range_B_other 15.367 r_mcbond_other 15.327 r_mcbond_it 15.323 r_long_range_B_refined 15.247 r_scangle_other 13.844 r_dihedral_angle_3_deg 12.812 r_scbond_it 8.207 r_scbond_other 8.203 r_dihedral_angle_1_deg 7.229 r_dihedral_angle_4_deg 7.189 r_angle_refined_deg 2.101 r_angle_other_deg 1.492 r_chiral_restr 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1809 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing