6YVP | pdb_00006yvp

Human histidine triad nucleotide-binding protein 2 (hHINT2) complexed with dGMP and refined to 2.77 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YQD	6YQD:B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	15 % (w/v) PEG6000, 5 % (v/v) glycerol

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.649	α = 90
b = 36.531	β = 103.034
c = 86.887	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 PILATUS 2M		2020-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	2.77	42.32	99.1	0.198	0.266	0.176	0.985	5.5	3.8		5698			31.4

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	2.77	2.92	99.1		0.668	0.894	0.589	0.799	2	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	6YQD:B	2.77	42.32	5695	565	98.649	0.218	0.2077	0.21	0.3077	0.31	34.978

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]
-1.837		1.086	5.134		-3.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.661
r_dihedral_angle_3_deg	19.373
r_dihedral_angle_4_deg	18.269
r_dihedral_angle_1_deg	6.486
r_lrange_it	4.975
r_lrange_other	4.973
r_mcangle_it	2.68
r_mcangle_other	2.679
r_scangle_other	2.411
r_scangle_it	2.409
r_mcbond_other	1.577
r_mcbond_it	1.576
r_angle_refined_deg	1.491
r_scbond_it	1.376
r_scbond_other	1.373
r_angle_other_deg	1.139
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.213
r_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.19
r_nbd_other	0.169
r_nbtor_refined	0.153
r_symmetry_nbd_refined	0.137
r_ncsr_local_group_1	0.126
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1756
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	46

Software

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