6MOK | pdb_00006mok

Dimeric DARPin A_distance_R7 complex with EpoR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERNpredicted model, 1ERN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52950.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
4.1470.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.09α = 90
b = 117.09β = 90
c = 233.587γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152018-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00001ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
15.10146.7998.380.1160.1230.039050.9969.929.84205
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
15.1015.28398.742.750.8840.5850.910.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEpredicted model, 1ERN5.10146.79378642198.620.232540.2250.250.29890.3RANDOM434.475
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]
3.951.973.95-12.81
RMS Deviations
KeyRefinement Restraint Deviation
r_mcangle_it60.08
r_scbond_it55.486
r_mcbond_it38.47
r_dihedral_angle_2_deg30.88
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg15.809
r_dihedral_angle_1_deg6.346
r_angle_refined_deg1.443
r_chiral_restr0.095
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_mcangle_it60.08
r_scbond_it55.486
r_mcbond_it38.47
r_dihedral_angle_2_deg30.88
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg15.809
r_dihedral_angle_1_deg6.346
r_angle_refined_deg1.443
r_chiral_restr0.095
r_bond_refined_d0.006
r_gen_planes_refined0.006
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
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3728
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing