4BGQ | pdb_00004bgq

Crystal structure of the human CDKL5 kinase domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BBM	PDB ENTRY 4BBM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				15% PEG SMEAR MEDIUM, 0.1M TRIS PH 8.0, 0.075M SODIUM ACETATE, 0.15M SODIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.942	α = 90
b = 65.507	β = 90
c = 102.899	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2013-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	55.02	99.2	0.07	22.6	12.2		23993		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	2.05	92.9		0.37	4.8	8.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4BBM	2	55.26	23136	1243	99.93	0.17517	0.17382	0.18	0.20135	0.19	RANDOM	28.581

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]
-14.7			4.05		10.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.526
r_dihedral_angle_4_deg	24.315
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	5.818
r_mcangle_it	2.713
r_scbond_it	1.881
r_mcbond_it	1.631
r_mcbond_other	1.615
r_angle_refined_deg	1.29
r_angle_other_deg	0.788
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
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	2196
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	44

Software

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