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Green fluorescent protein from Clytia gregaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QV1 PDB ENTRY 1QV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 2 microlitre drops containing protein containing equal volumes of protein solution (9 mg/ml) and precipitate solution (2.0M Ammonium sulfate, 0.1M Citrate), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.091 α = 90 b = 91.446 β = 90 c = 110.612 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE MAR scanner 300 mm plate Rosenbaum 2005-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.47 27.7 86.7 0.049 14.7 4.4 40289 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.52 20.3 0.145 1.5 927
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QV1 1.55 10 36117 36117 1877 96.69 0.18271 0.18271 0.18169 0.1813 0.20254 RANDOM 14.265
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] 0.32 -0.04 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_3_deg 11.83 r_dihedral_angle_4_deg 11.813 r_dihedral_angle_1_deg 6.341 r_scangle_it 3.056 r_mcangle_it 2.485 r_scbond_it 2.108 r_mcbond_it 1.82 r_angle_refined_deg 1.407 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_3_deg 11.83 r_dihedral_angle_4_deg 11.813 r_dihedral_angle_1_deg 6.341 r_scangle_it 3.056 r_mcangle_it 2.485 r_scbond_it 2.108 r_mcbond_it 1.82 r_angle_refined_deg 1.407 r_nbtor_refined 0.305 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1827 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing