8QW2 | pdb_00008qw2

Human NDPK-C in complex with UDP 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
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.532	α = 90
b = 115.991	β = 93.281
c = 83.842	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 EIGER2 X CdTe 16M	Toroidal mirror	2021-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.6888	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	1.87	47.717	99.9	0.042	0.047	0.02	0.997	15	5.2		83689			44

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	1.87	1.94	99.5		1.187	1.331	0.592	0.697	1.1	4.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.87	47.717	83594	2091	99.722	0.171	0.1704	0.1814	0.2026	0.2094	58.175

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]
0.04		2.016	-0.875		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.211
r_dihedral_angle_6_deg	14.884
r_dihedral_angle_2_deg	10.638
r_lrange_other	9.092
r_lrange_it	9.083
r_scangle_it	7.505
r_scangle_other	7.504
r_dihedral_angle_1_deg	6.499
r_scbond_other	5.254
r_scbond_it	5.251
r_mcangle_it	4.56
r_mcangle_other	4.531
r_mcbond_it	3.548
r_mcbond_other	3.544
r_angle_refined_deg	1.618
r_angle_other_deg	0.514
r_nbd_refined	0.217
r_symmetry_nbd_other	0.19
r_nbd_other	0.184
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.166
r_symmetry_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.129
r_metal_ion_refined	0.087
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_7	0.081
r_ncsr_local_group_5	0.079
r_ncsr_local_group_2	0.076
r_ncsr_local_group_1	0.075
r_ncsr_local_group_11	0.075
r_ncsr_local_group_13	0.075
r_chiral_restr	0.074
r_ncsr_local_group_8	0.073
r_ncsr_local_group_3	0.072
r_ncsr_local_group_4	0.072
r_ncsr_local_group_10	0.072
r_ncsr_local_group_12	0.072
r_ncsr_local_group_14	0.066
r_ncsr_local_group_6	0.064
r_ncsr_local_group_9	0.064
r_ncsr_local_group_15	0.056
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	313
Heterogen Atoms	156

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing