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Structure of the Yellow Fluorescent Protein Citrine Frozen at 1000 Atmospheres Number 6: Structure 10 in a Series of 26 High Pressure Structures
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUY PDB entry 1HUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.45 α = 90 b = 62.272 β = 90 c = 70.366 γ = 90
Symmetry Space Group P 21 21 21
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 210 2006-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9795 CHESS F2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.46 41.53 72.4 0.071 0.071 7.3 4.1 28943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.46 99.8 0.26 0.26 2.7 3.7
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 1HUY 1.46 20 27490 1433 72.1 0.19841 0.19594 0.1947 0.24435 0.2437 RANDOM 21.307
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] -0.07 -0.01 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.851 r_dihedral_angle_3_deg 16.242 r_dihedral_angle_4_deg 13.175 r_dihedral_angle_1_deg 7.277 r_scangle_it 5.939 r_scbond_it 4.357 r_mcangle_it 2.389 r_angle_refined_deg 2.388 r_mcbond_it 2.144 r_symmetry_hbond_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.851 r_dihedral_angle_3_deg 16.242 r_dihedral_angle_4_deg 13.175 r_dihedral_angle_1_deg 7.277 r_scangle_it 5.939 r_scbond_it 4.357 r_mcangle_it 2.389 r_angle_refined_deg 2.388 r_mcbond_it 2.144 r_symmetry_hbond_refined 0.312 r_nbtor_refined 0.305 r_nbd_refined 0.273 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.176 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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 1850 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction