3DQU

Structure of the Yellow Fluorescent Protein Citrine Frozen at 2000 Atmospheres Number 1: Structure 20 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 WITH RESIDUE 80 MUTATED TO GLUTAMINE

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
2.141.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.428α = 90
b = 62.944β = 90
c = 71.205γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-02-24MSINGLE 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
11.4241.6968.80.0780.0786.37.830497
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)
1.4258.40.0360.8840.94.7

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 1HUY WITH RESIDUE 80 MUTATED TO GLUTAMINE1.422028898157768.410.206710.203940.25652RANDOM24.245
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]
-0.13-0.020.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.516
r_dihedral_angle_3_deg16.583
r_dihedral_angle_4_deg15.452
r_dihedral_angle_1_deg7.36
r_scangle_it6.079
r_scbond_it4.389
r_mcangle_it2.487
r_angle_refined_deg2.393
r_mcbond_it2.284
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.516
r_dihedral_angle_3_deg16.583
r_dihedral_angle_4_deg15.452
r_dihedral_angle_1_deg7.36
r_scangle_it6.079
r_scbond_it4.389
r_mcangle_it2.487
r_angle_refined_deg2.393
r_mcbond_it2.284
r_nbtor_refined0.304
r_nbd_refined0.277
r_symmetry_vdw_refined0.232
r_xyhbond_nbd_refined0.201
r_chiral_restr0.145
r_symmetry_hbond_refined0.129
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 Atoms280
Heterogen Atoms

Software

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