3BHY | pdb_00003bhy

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with a beta-carboline ligand

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YRP	PDB entry 1YRP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	0.1M SPG (sucrose-phosphate-glutamate buffer) pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.549	α = 90
b = 90.68	β = 100.45
c = 41.464	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	CCD	MARMOSAIC 225 mm CCD		2007-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97926	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.24	50	99.5	0.079	0.079	14.7	3.7	68642	68318

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.24	1.28	100		0.707	0.707	2.04	3.6	6829

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YRP	1.24	45.36	68317	68317	3453	99.53	0.146	0.146	0.143	0.14	0.187	RANDOM	15.982

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]
0.34		-0.06	-0.42		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.863
r_sphericity_free	19.814
r_dihedral_angle_4_deg	19.334
r_dihedral_angle_3_deg	12.942
r_scangle_it	10.898
r_scbond_it	8.964
r_sphericity_bonded	8.856
r_mcangle_it	6.382
r_dihedral_angle_1_deg	5.657
r_mcbond_it	5.528
r_rigid_bond_restr	4.887
r_mcbond_other	3.402
r_angle_other_deg	1.996
r_angle_refined_deg	1.703
r_nbd_refined	0.249
r_symmetry_vdw_other	0.219
r_nbd_other	0.192
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.128
r_nbtor_other	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2109
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	26

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction