5PKG

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 101)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729828% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.522α = 90
b = 71.522β = 90
c = 150.607γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

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
11.5429.4499.60.0930.0970.0270.99816.512.458049
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)
11.541.5793.60.770.8080.2380.81710.62842

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4D6R1.5429.4455152280799.60.15370.15230.1801RANDOM18.518
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.283
r_dihedral_angle_4_deg18.059
r_dihedral_angle_3_deg11.754
r_dihedral_angle_1_deg6.501
r_mcangle_it2.552
r_angle_refined_deg2.173
r_mcbond_it1.802
r_mcbond_other1.79
r_angle_other_deg1.133
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.283
r_dihedral_angle_4_deg18.059
r_dihedral_angle_3_deg11.754
r_dihedral_angle_1_deg6.501
r_mcangle_it2.552
r_angle_refined_deg2.173
r_mcbond_it1.802
r_mcbond_other1.79
r_angle_other_deg1.133
r_chiral_restr0.136
r_bond_refined_d0.024
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2664
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing