5RAH

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010032a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52770.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.7855.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.37α = 90
b = 93.59β = 107.85
c = 93.58γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-09-30SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.92819DiamondI02

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
11.6689.0899.10.0750.0890.0480.9978.83.4109887
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)
11.661.7991.131.3440.7180.4673.48144

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 SYNTHESISTHROUGHOUT6RBJ1.6689.08104305555898.960.18150.18030.2052RANDOM31.447
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]
1.57-0.05-1.21-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.433
r_dihedral_angle_4_deg21.174
r_dihedral_angle_3_deg14.702
r_dihedral_angle_1_deg7.402
r_mcangle_it4.667
r_mcbond_other3.007
r_mcbond_it3
r_angle_refined_deg1.716
r_angle_other_deg1.356
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.433
r_dihedral_angle_4_deg21.174
r_dihedral_angle_3_deg14.702
r_dihedral_angle_1_deg7.402
r_mcangle_it4.667
r_mcbond_other3.007
r_mcbond_it3
r_angle_refined_deg1.716
r_angle_other_deg1.356
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5510
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing