9KNF | pdb_00009knf

Crystal structure of human ERRg LBD in complex with 4028691


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GPO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.0 M K/Na tartrate, 0.1 M Tris pH 7.0, 0.2 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.2α = 90
b = 64.2β = 90
c = 138.87γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97875SSRFBL17U1

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
11.6264.291.70.0960.0980.020.99921.423.534901
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.6499.91.2921.3180.2610.81524.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6258.2732711168190.490.174910.1720.18170.22770.241RANDOM27.376
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]
2.172.17-4.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.149
r_dihedral_angle_4_deg17.778
r_dihedral_angle_3_deg14.26
r_scangle_other7.1
r_long_range_B_other6.734
r_long_range_B_refined6.73
r_rigid_bond_restr6.257
r_scbond_it6.051
r_scbond_other6.047
r_mcangle_other5.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.149
r_dihedral_angle_4_deg17.778
r_dihedral_angle_3_deg14.26
r_scangle_other7.1
r_long_range_B_other6.734
r_long_range_B_refined6.73
r_rigid_bond_restr6.257
r_scbond_it6.051
r_scbond_other6.047
r_mcangle_other5.526
r_mcangle_it5.504
r_dihedral_angle_1_deg5.34
r_mcbond_it4.919
r_mcbond_other4.731
r_angle_refined_deg1.804
r_angle_other_deg1.48
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1885
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOSFLMdata reduction
MOLREPphasing