5PKA

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 95)


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
2.2846.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.401α = 90
b = 71.401β = 90
c = 150.375γ = 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
11.7129.3999.50.070.0730.02128.712.742587
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)
11.711.7490.60.8610.9020.260.86110.92025

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 SYNTHESISTHROUGHOUT4D6R1.7129.3940456205399.620.14870.14710.18RANDOM21.947
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]
0.580.58-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.42
r_dihedral_angle_4_deg18.669
r_dihedral_angle_3_deg11.909
r_dihedral_angle_1_deg6.496
r_mcangle_it2.685
r_angle_refined_deg1.942
r_mcbond_it1.941
r_mcbond_other1.932
r_angle_other_deg1.091
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.42
r_dihedral_angle_4_deg18.669
r_dihedral_angle_3_deg11.909
r_dihedral_angle_1_deg6.496
r_mcangle_it2.685
r_angle_refined_deg1.942
r_mcbond_it1.941
r_mcbond_other1.932
r_angle_other_deg1.091
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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