4C8D

Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YPDPDB ENTRY 2YPD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M BIS-TRIS PH 5.5, 0.1M AMMONIUM ACETATE, 27% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.34α = 90
b = 85.61β = 90
c = 117.13γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.1869.1299.90.0512.24.3222312.8
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)
12.182.2599.70.382.83.5

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2YPD2.1869.1220691111097.960.196510.19430.23911RANDOM61.731
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]
-3.26-5.388.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_3_deg14.558
r_dihedral_angle_4_deg11.543
r_dihedral_angle_1_deg5.96
r_mcangle_it5.426
r_scbond_it4.75
r_mcbond_it4.025
r_mcbond_other3.998
r_angle_refined_deg1.165
r_angle_other_deg0.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_3_deg14.558
r_dihedral_angle_4_deg11.543
r_dihedral_angle_1_deg5.96
r_mcangle_it5.426
r_scbond_it4.75
r_mcbond_it4.025
r_mcbond_other3.998
r_angle_refined_deg1.165
r_angle_other_deg0.745
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_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 Atoms2558
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing