4GF6

crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino Acid PYZ151


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GES 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.928960~100mg/ml protein sample in 50 mM Hepes, pH 7.5, reservior solution:17~19% PEG 3000, 100mM Tris pH 8.9,0.2M calcium acetate , VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.141.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.827α = 90
b = 63.052β = 90
c = 70.369γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 3152012-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

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
11.13099.10.08821.16.2924489161611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1499.50.3426.96.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4GES1.1308790187031457699.010.166670.166020.179RANDOM11.058
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]
0.02-0.180.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_3_deg12.352
r_dihedral_angle_4_deg8.057
r_dihedral_angle_1_deg6.218
r_sphericity_free4.829
r_sphericity_bonded3.017
r_scangle_it2.899
r_scbond_it1.985
r_mcangle_it1.764
r_angle_refined_deg1.465
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_3_deg12.352
r_dihedral_angle_4_deg8.057
r_dihedral_angle_1_deg6.218
r_sphericity_free4.829
r_sphericity_bonded3.017
r_scangle_it2.899
r_scbond_it1.985
r_mcangle_it1.764
r_angle_refined_deg1.465
r_mcbond_it1.105
r_rigid_bond_restr1.049
r_chiral_restr0.106
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1916
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing