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Crystal structure analysis of a single amino acid deletion mutation in EGFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EUL PDB Entry 4EUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 0.1 M Na cacodylate, 0.2 M NaCl, 1M Na citrate, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.14 α = 90 b = 57.14 β = 90 c = 135.33 γ = 120
Symmetry Space Group P 32 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.12 39.94 97.3 9.1 91397
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 PDB Entry 4EUL 1.12 39.94 89439 4723 96.12 0.14509 0.14426 0.1534 0.16108 0.1737 RANDOM 15.08
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] 0.13 0.13 0.13 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.13 r_rigid_bond_restr 10.307 r_dihedral_angle_1_deg 7.925 r_angle_other_deg 3.936 r_angle_refined_deg 2.715 r_sphericity_bonded 1.217 r_chiral_restr 0.148 r_bond_refined_d 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_3_deg 13.13 r_rigid_bond_restr 10.307 r_dihedral_angle_1_deg 7.925 r_angle_other_deg 3.936 r_angle_refined_deg 2.715 r_sphericity_bonded 1.217 r_chiral_restr 0.148 r_bond_refined_d 0.03 r_gen_planes_other 0.024 r_gen_planes_refined 0.013 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1802 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 98
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction