3ZDU

Crystal structure of the human CDKL3 kinase domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.03M ZN CL, 30% PEG_6000, 5% ETHYLENE GLYCOL, MES PH5.5

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.93	α = 90
b = 63.93	β = 90
c = 163.63	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC CCD		2012-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	54.54	99.9	0.1	10.7	5.2		20446		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	100		0.63	2.5	2.5

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	MOLECULAR REPLACEMENT	THROUGHOUT	ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA	2.2	45.89	18821	1013	97.1	0.21662	0.21425	0.26248	RANDOM	55.118

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]
1.27	1.27		1.27		-4.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.15
r_dihedral_angle_4_deg	24.066
r_dihedral_angle_3_deg	14.956
r_dihedral_angle_1_deg	6.554
r_mcangle_it	1.823
r_scbond_it	1.763
r_angle_refined_deg	1.51
r_mcbond_it	1.143
r_mcbond_other	1.142
r_angle_other_deg	0.793
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2319
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing