6YPX

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 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	6.5	281	0.2 M sodium citrate, 0.1 M sodium cacodylate, 30 % 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.411	α = 90
b = 153.992	β = 90
c = 74.785	γ = 90

Symmetry
Space Group	C 2 2 21

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		2013-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9669	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	2.11	102.94	99.6	0.22	0.24	0.094	0.994	11.3	12.2		46164			15.482

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	2.11	2.17	96.4		1.041	1.194	0.568	0.697	2	7.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3TW2	2.11	102.94	46144	2349	99.59	0.149	0.1476	0.1845	25.345

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]
0.105			1.922		-2.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.528
r_dihedral_angle_4_deg	19.916
r_dihedral_angle_3_deg	13.285
r_lrange_it	7.575
r_lrange_other	7.256
r_dihedral_angle_1_deg	6.592
r_scangle_it	4.936
r_scangle_other	4.935
r_scbond_it	3.242
r_scbond_other	3.242
r_mcangle_it	2.988
r_mcangle_other	2.988
r_mcbond_it	2.021
r_mcbond_other	2.018
r_angle_refined_deg	1.613
r_angle_other_deg	1.407
r_nbd_refined	0.229
r_nbd_other	0.207
r_symmetry_xyhbond_nbd_refined	0.201
r_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.158
r_symmetry_nbd_refined	0.136
r_ncsr_local_group_1	0.092
r_chiral_restr	0.088
r_ncsr_local_group_6	0.086
r_ncsr_local_group_3	0.085
r_ncsr_local_group_5	0.083
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_2	0.081
r_ncsr_local_group_4	0.071
r_bond_refined_d	0.012
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	3532
Nucleic Acid Atoms
Solvent Atoms	674
Heterogen Atoms	24

Software

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