4KEX

Crystal structure analysis of a single amino acid deletion mutation in EGFP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EULPDB ENTRY 4EUL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION42910.1 M MMT Buffer (Malic acid, MES and Tris), 25% (w/v) PEG 1500, pH 4.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9838.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.45α = 90
b = 63.14β = 90
c = 65.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97630DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.651.4598.10.09215.27.92820913.4

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 4EUL1.645.5728165141797.770.18370.18230.2092RANDOM17.9795
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]
-0.220.28-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg15.534
r_dihedral_angle_3_deg14.847
r_dihedral_angle_1_deg6.942
r_angle_refined_deg2.139
r_angle_other_deg0.939
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg15.534
r_dihedral_angle_3_deg14.847
r_dihedral_angle_1_deg6.942
r_angle_refined_deg2.139
r_angle_other_deg0.939
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.006
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1804
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction