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Crystal Structure of N66D Mutant of Green Fluorescent Protein from Zoanthus sp. at 2.4 A Resolution (Transition State)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FL1 zGFP506
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 1.9 M Na Malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.94 68.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.204 α = 90 b = 102.204 β = 90 c = 269.375 γ = 120
Symmetry Space Group P 62 2 2
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 MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 30 100 0.096 8.5 13.5 33832
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) 2.4 2.49 100 0.62 13.3 3287
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 zGFP506 2.4 29.32 33355 1694 99.6 0.167 0.166 0.1649 0.2 0.2002 RANDOM 33.705
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] 0.09 0.04 0.09 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 19.864 r_dihedral_angle_3_deg 16.739 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.817 r_scbond_it 2.955 r_mcangle_it 1.876 r_angle_refined_deg 1.704 r_mcbond_it 1.054 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 19.864 r_dihedral_angle_3_deg 16.739 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.817 r_scbond_it 2.955 r_mcangle_it 1.876 r_angle_refined_deg 1.704 r_mcbond_it 1.054 r_nbtor_refined 0.309 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3670 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction