6YPR | pdb_00006ypr

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.26 A in H32 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	281	0.8 M Na/K Tartrate, 0.1 M HEPES 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.076	α = 90
b = 72.076	β = 90
c = 103.576	γ = 120

Symmetry
Space Group	H 3 2

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		2016-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0332	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.26	36.043	99.8	0.058	0.073	0.043	0.998	12.6	4.8		28102			9.5

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	1.26	1.28	99.8		0.645	0.815	0.492	0.685	2	4.5

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	3TW2	1.26	36.043	28101	1375	99.73	0.118	0.1171	0.12	0.1427	0.15	13.669

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]
-0.665	-0.333		-0.665		2.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.908
r_dihedral_angle_4_deg	17.379
r_dihedral_angle_3_deg	11.131
r_rigid_bond_restr	10.479
r_dihedral_angle_1_deg	6.33
r_lrange_it	4.609
r_scangle_it	3.856
r_scangle_other	3.854
r_lrange_other	3.816
r_scbond_it	3.354
r_scbond_other	3.351
r_angle_refined_deg	2.077
r_mcangle_it	1.68
r_mcangle_other	1.679
r_angle_other_deg	1.611
r_mcbond_other	1.345
r_mcbond_it	1.342
r_symmetry_nbd_refined	0.906
r_symmetry_xyhbond_nbd_refined	0.403
r_nbd_refined	0.211
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.166
r_nbd_other	0.162
r_chiral_restr	0.141
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.018
r_symmetry_xyhbond_nbd_other	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.01
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	756
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	18

Software

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