5RAK

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS040486b

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.59	α = 90
b = 93.46	β = 107.94
c = 94.182	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2015-09-30		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.92819	Diamond	I02

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.69	64.68	98.7	0.058	0.069	0.037	0.998	12.4	3.4		104570

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)	Redundancy	Number Unique Reflections (All)
1	1.69	1.73	98.4		0.907	1.083	0.583	0.518		3.3	7662

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6RBJ	1.69	64.76	99209	5334	98.56	0.1833	0.1817	0.2127	RANDOM	31.198

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]
0.74		-0.14	-1.12		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.152
r_dihedral_angle_4_deg	19.372
r_dihedral_angle_3_deg	14.726
r_dihedral_angle_1_deg	7.514
r_mcangle_it	4.643
r_mcbond_other	3.081
r_mcbond_it	3.071
r_angle_refined_deg	1.729
r_angle_other_deg	1.339
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5510
Nucleic Acid Atoms
Solvent Atoms	704
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing