8QW1

Human NDPK-C in complex with ADP and Mg2+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of ADP complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	27% glycerol, 7% PEG 8000, 40 mM KH2PO4

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.46	α = 90
b = 116.31	β = 93.054
c = 84.07	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS3 X 2M	KB mirror	2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	42.011	95.8	0.184	0.199	0.995	10.01	6.6		57087			41.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	73.1		1.509	1.659	0.466	1.72	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	42.011	57087	2382	95.821	0.174	0.1722	0.2045	39.151

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]
0.344		0.735	-0.853		0.429

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.973
r_dihedral_angle_6_deg	15.579
r_dihedral_angle_2_deg	10.875
r_lrange_it	7.94
r_lrange_other	7.927
r_scangle_other	6.526
r_scangle_it	6.525
r_dihedral_angle_1_deg	6.469
r_scbond_it	4.283
r_scbond_other	4.283
r_mcangle_it	3.737
r_mcangle_other	3.718
r_mcbond_it	2.654
r_mcbond_other	2.653
r_angle_refined_deg	1.641
r_angle_other_deg	0.516
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.203
r_nbd_other	0.198
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.164
r_dihedral_angle_other_2_deg	0.131
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_refined	0.075
r_ncsr_local_group_4	0.075
r_ncsr_local_group_2	0.074
r_ncsr_local_group_11	0.073
r_ncsr_local_group_5	0.072
r_ncsr_local_group_7	0.072
r_ncsr_local_group_1	0.071
r_ncsr_local_group_13	0.071
r_ncsr_local_group_3	0.07
r_ncsr_local_group_8	0.07
r_ncsr_local_group_10	0.07
r_ncsr_local_group_12	0.069
r_ncsr_local_group_14	0.066
r_ncsr_local_group_6	0.064
r_ncsr_local_group_9	0.062
r_metal_ion_refined	0.061
r_ncsr_local_group_15	0.051
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7284
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms	168

Software

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