3DQF

Structure of the Yellow Fluorescent Protein Citrine Frozen at 1000 Atmospheres Number 6: Structure 10 in a Series of 26 High Pressure Structures


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HUYPDB entry 1HUY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5277Crystals 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 coefficientSolvent content
2.0640.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.45α = 90
b = 62.272β = 90
c = 70.366γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.9795CHESSF2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4641.5372.40.0710.0717.34.128943
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)RedundancyNumber Unique Reflections (All)
1.4699.80.260.262.73.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1HUY1.462027490143372.10.198410.195940.24435RANDOM21.307
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]
-0.07-0.010.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.851
r_dihedral_angle_3_deg16.242
r_dihedral_angle_4_deg13.175
r_dihedral_angle_1_deg7.277
r_scangle_it5.939
r_scbond_it4.357
r_mcangle_it2.389
r_angle_refined_deg2.388
r_mcbond_it2.144
r_symmetry_hbond_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.851
r_dihedral_angle_3_deg16.242
r_dihedral_angle_4_deg13.175
r_dihedral_angle_1_deg7.277
r_scangle_it5.939
r_scbond_it4.357
r_mcangle_it2.389
r_angle_refined_deg2.388
r_mcbond_it2.144
r_symmetry_hbond_refined0.312
r_nbtor_refined0.305
r_nbd_refined0.273
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.183
r_chiral_restr0.176
r_bond_refined_d0.029
r_gen_planes_refined0.013
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 AtomsNumber
Protein Atoms1850
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction