1HHQ | pdb_00001hhq

Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH7.5, 1 M AS, 20MM MGCL2 IN WELL: 2M AS, 50MM TRISHCL PH7.5, 20MM MGCL2, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.4	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.15	α = 90
b = 72.15	β = 90
c = 107	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.1	20	99.7	0.05	10.1	4.3		11016		2	18

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1NPK	2.1	20	2	10966	1092	99	0.177	0.177	0.18	0.255	RANDOM	18.7

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	25
x_angle_deg	1.2
x_improper_angle_d	0.65
x_bond_d	0.006
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1143
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	5

Software

Software
Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing