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Structure of the Yellow Fluorescent Protein Citrine Frozen at 4000 Atmospheres Number 1: Structure 23 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 2.05 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.366 α = 90 b = 69.993 β = 89.98 c = 62.499 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 1.6 41.42 90.9 0.068 0.068 7.4 6.9 27664
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) 1.6 99.4 0.276 0.276 2.7 6.2
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 1.6 20 26250 1392 90.96 0.22427 0.22123 0.2161 0.28213 0.2772 RANDOM 19.403
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] -0.1 0.12 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_3_deg 16.413 r_dihedral_angle_4_deg 7.306 r_dihedral_angle_1_deg 7.143 r_scangle_it 6.116 r_scbond_it 4.248 r_mcangle_it 2.48 r_angle_refined_deg 2.321 r_mcbond_it 2.077 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_3_deg 16.413 r_dihedral_angle_4_deg 7.306 r_dihedral_angle_1_deg 7.143 r_scangle_it 6.116 r_scbond_it 4.248 r_mcangle_it 2.48 r_angle_refined_deg 2.321 r_mcbond_it 2.077 r_nbtor_refined 0.31 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.167 r_symmetry_hbond_refined 0.136 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 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 213 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction