4RXW | pdb_00004rxw

Crystal Structure of the cobalt human insulin derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MSO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.4293the protein solution consisted 7.5 mg mL-1 Zn-free insulin in 0.02 M HCl, while the reservoir solution contained 1 mM solution of sodium citrate, pH 6.4, (acetone) = 10 %, 16,5 mM solution of cobalt(II) acetate and redistilled water, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8533.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.43α = 90
b = 81.43β = 90
c = 33.75γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.732099.20.0690.0578676

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1MSO1.7320821045399.460.146120.142810.150.205990.21RANDOM17.818
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]
0.050.030.05-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_3_deg14.238
r_sphericity_free13.528
r_dihedral_angle_4_deg8.924
r_dihedral_angle_1_deg6.998
r_long_range_B_refined6.246
r_long_range_B_other6.069
r_scangle_other3.643
r_mcangle_it2.522
r_mcangle_other2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_3_deg14.238
r_sphericity_free13.528
r_dihedral_angle_4_deg8.924
r_dihedral_angle_1_deg6.998
r_long_range_B_refined6.246
r_long_range_B_other6.069
r_scangle_other3.643
r_mcangle_it2.522
r_mcangle_other2.52
r_scbond_it2.319
r_scbond_other2.317
r_angle_refined_deg1.797
r_mcbond_it1.61
r_mcbond_other1.598
r_angle_other_deg0.931
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms806
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing