9KNG | pdb_00009kng

Crystal structure of human ERRg LBD in complex with 4034496


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330%(w/v) PEG 5000 MME, 0.1M Tris 8.0, 0.2M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.3748.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.292α = 90
b = 64.292β = 90
c = 137.907γ = 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
11.564.2999.90.060.0610.0120.99929.32447222
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)
11.51.5399.10.8890.9210.2310.86114.7

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 REPLACEMENTTHROUGHOUT1.547.0744782231799.810.193570.191530.19990.23350.2374RANDOM25.047
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]
-0.43-0.430.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.646
r_dihedral_angle_4_deg18.397
r_dihedral_angle_3_deg14.182
r_long_range_B_refined6.176
r_long_range_B_other6.021
r_dihedral_angle_1_deg5.194
r_scangle_other5.146
r_scbond_it3.456
r_scbond_other3.456
r_mcangle_it3.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.646
r_dihedral_angle_4_deg18.397
r_dihedral_angle_3_deg14.182
r_long_range_B_refined6.176
r_long_range_B_other6.021
r_dihedral_angle_1_deg5.194
r_scangle_other5.146
r_scbond_it3.456
r_scbond_other3.456
r_mcangle_it3.048
r_mcangle_other3.047
r_mcbond_it2.193
r_mcbond_other2.193
r_angle_refined_deg1.932
r_angle_other_deg1.56
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1853
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing