8QW3

Human NDPK-C in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.4	291	6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.315	α = 108.492
b = 67.865	β = 112.343
c = 68.423	γ = 101.105

Symmetry
Space Group	P 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 PILATUS 6M-F	Toroidal mirror	2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0052	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.25	60.12	94.2	0.049	0.06	0.033	0.97	8.6	2.8		198602			12.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.28	89		0.947	1.339	0.947	0.401	0.7	1.8

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	1.255	60.119	198505	2119	94.108	0.147	0.1467	0.1755	19.87

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]
-0.238	-0.167	-0.151	-0.071	-0.243	0.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.308
r_lrange_it	16.293
r_lrange_other	15.884
r_dihedral_angle_6_deg	15.609
r_dihedral_angle_3_deg	14.919
r_scangle_it	12.325
r_scangle_other	12.324
r_mcangle_other	8.761
r_mcangle_it	8.76
r_scbond_it	8.6
r_scbond_other	8.6
r_dihedral_angle_1_deg	6.378
r_mcbond_it	6.148
r_mcbond_other	6.127
r_rigid_bond_restr	4.395
r_angle_refined_deg	1.671
r_dihedral_angle_other_2_deg	1.355
r_angle_other_deg	0.916
r_nbd_other	0.41
r_symmetry_nbd_refined	0.389
r_nbd_refined	0.224
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.057
r_gen_planes_other	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7253
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms	177

Software

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