2HVD | pdb_00002hvd

Human nucleoside diphosphate kinase A complexed with ADP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UCN	PDB ENTRY 1UCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	2.4 M AMMONIUM SULPHATE,10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.26	α = 90
b = 114.26	β = 90
c = 89.789	γ = 90

Symmetry
Space Group	P 41 21 2

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	MARRESEARCH		2005-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.973	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15	17.65	97.2	0.08	10.2	3.2	30827	30827			39.084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.27	99		0.52	3.1	3.1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UCN	2.15	17.65	30827	30827	1639	98.75	0.24911	0.24911	0.24672	0.26	0.29374	0.3	RANDOM	42.196

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]
-0.69			-0.69		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.739
r_dihedral_angle_4_deg	22.99
r_dihedral_angle_3_deg	14.412
r_dihedral_angle_1_deg	6.298
r_scangle_it	2.084
r_scbond_it	1.514
r_angle_refined_deg	1.299
r_mcbond_it	1.132
r_mcangle_it	1.033
r_angle_other_deg	0.787
r_symmetry_vdw_refined	0.388
r_symmetry_vdw_other	0.202
r_nbd_refined	0.197
r_nbd_other	0.194
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.172
r_mcbond_other	0.1
r_symmetry_hbond_refined	0.088
r_nbtor_other	0.084
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.021
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3594
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	81

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling