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Structure of the Yellow Fluorescent Protein Citrine Frozen at 4000 Atmospheres Number 3: Structure 25 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 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.531 α = 90 b = 62.653 β = 90 c = 71.471 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 2007-04-05 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 1.7 41.81 97.4 0.069 0.069 8.6 6.6 25414
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) 1.7 99.9 0.259 0.259 2.9 6.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1HUY 1.7 20 24113 1299 97.41 0.22385 0.22011 0.2189 0.2944 RANDOM 23.531
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] -0.06 -0.04 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.525 r_dihedral_angle_3_deg 17.419 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_1_deg 7.554 r_scangle_it 5.86 r_scbond_it 4.052 r_mcangle_it 2.432 r_mcbond_it 2.422 r_angle_refined_deg 2.273 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.525 r_dihedral_angle_3_deg 17.419 r_dihedral_angle_4_deg 16.911 r_dihedral_angle_1_deg 7.554 r_scangle_it 5.86 r_scbond_it 4.052 r_mcangle_it 2.432 r_mcbond_it 2.422 r_angle_refined_deg 2.273 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.266 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.163 r_symmetry_hbond_refined 0.14 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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 205 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction