5F5C

Crystal Structure of human JMJD2D complexed with KDOPP7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.829326% PEG3350 , 0.1M HEPES pH 6.8 , 0.2M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.4149.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.594α = 90
b = 71.594β = 90
c = 150.79γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352014-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.8864.6899.80.12913.510.43269832698-3-3
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)
11.881.9297.50.5181.963.95

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 REPLACEMENTTHROUGHOUT4d6q1.8851.9230964163599.610.17340.17150.2108RANDOM13.863
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.222
r_dihedral_angle_4_deg21.992
r_dihedral_angle_3_deg14.107
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.693
r_angle_other_deg1.002
r_mcangle_it1
r_mcbond_it0.572
r_mcbond_other0.572
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.222
r_dihedral_angle_4_deg21.992
r_dihedral_angle_3_deg14.107
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.693
r_angle_other_deg1.002
r_mcangle_it1
r_mcbond_it0.572
r_mcbond_other0.572
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2665
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms57

Software

Software
Software NamePurpose
SADABSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
REFMACphasing