5PKY

PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 119)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2012-12-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97630
Spacegroup name	P 43 21 2
Unit cell lengths	71.422, 71.422, 150.270
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	29.390 - 1.250
R-factor	0.1622
Rwork	0.161
R-free	0.18060
Structure solution method	FOURIER SYNTHESIS
Starting model (for MR)	4d6r
RMSD bond length	0.028
RMSD bond angle	2.440
Data reduction software	XDS
Data scaling software	Aimless (0.1.27)
Phasing software	REFMAC
Refinement software	REFMAC (5.8.0131)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	29.390	29.390	1.270
High resolution limit [Å]	1.250	6.850	1.250
Rmerge	0.073	0.067	0.618
Rmeas	0.076	0.070	0.760
Rpim	0.022	0.021	0.433
Total number of observations	1098826	8801	11201
Number of reflections	106582
<I/σ(I)>	18	40.2	1.5
Completeness [%]	98.7	98.8	83.7
Redundancy	10.3	11.1	2.6
CC(1/2)	0.998	0.987	0.638

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	298	28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate