8QVY | pdb_00008qvy

Human NDPK-C unliganded

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
2.4	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.23	α = 90
b = 115.51	β = 94.316
c = 82.61	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 EIGER X 4M	Vertical CRL / horizontal eliptical mirror	2021-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	2.64	47.335	96.4	0.127	0.137	0.992	9.45	7.3		28215			79.1

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	2.64	2.71	98.2		2.39	2.571	0.48	0.92	7.4

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	2.64	47.335	28215	1263	96.382	0.199	0.1972	0.2022	0.2469	0.2456	98.163

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]
-1.433		5.525	-3.702		4.252

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.641
r_dihedral_angle_2_deg	14.102
r_dihedral_angle_6_deg	13.8
r_lrange_it	13.029
r_lrange_other	13.028
r_scangle_it	10.455
r_scangle_other	10.434
r_mcangle_it	9.322
r_mcangle_other	9.321
r_dihedral_angle_1_deg	7.423
r_scbond_it	7.037
r_scbond_other	7.015
r_mcbond_it	6.231
r_mcbond_other	6.231
r_angle_refined_deg	1.47
r_angle_other_deg	0.503
r_symmetry_xyhbond_nbd_refined	0.316
r_nbd_refined	0.22
r_nbd_other	0.207
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.153
r_symmetry_nbd_refined	0.111
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_7	0.068
r_ncsr_local_group_2	0.067
r_ncsr_local_group_14	0.067
r_ncsr_local_group_1	0.066
r_ncsr_local_group_8	0.065
r_ncsr_local_group_11	0.064
r_ncsr_local_group_4	0.063
r_ncsr_local_group_12	0.062
r_chiral_restr	0.061
r_ncsr_local_group_10	0.061
r_ncsr_local_group_5	0.06
r_ncsr_local_group_13	0.06
r_ncsr_local_group_15	0.057
r_ncsr_local_group_6	0.054
r_ncsr_local_group_3	0.051
r_ncsr_local_group_9	0.05
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7073
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	30

Software

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