8WZC | pdb_00008wzc

NYN domain of human KHNYN complex with RNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Tris-HCl, PEG4000, calcium chloride, 1-Propanol

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.197	α = 90
b = 111.197	β = 90
c = 111.197	γ = 90

Symmetry
Space Group	P 41 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 EIGER X 9M		2023-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97495	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.92	50	99.9	0.999	53.2875	104		18429

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95			0.424

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	SAD	FREE R-VALUE	1.925	49.729	18391	976	99.891	0.181	0.1797	0.1915	0.2094	0.2204	39.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.229
r_lrange_it	14.463
r_lrange_other	14.46
r_dihedral_angle_3_deg	13.263
r_dihedral_angle_2_deg	13.183
r_scangle_it	10.042
r_scangle_other	10.038
r_dihedral_angle_1_deg	7.146
r_scbond_it	6.277
r_scbond_other	6.273
r_mcangle_it	6.221
r_mcangle_other	6.218
r_mcbond_it	4.028
r_mcbond_other	4.022
r_angle_refined_deg	1.583
r_angle_other_deg	0.52
r_nbd_other	0.303
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.211
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.159
r_dihedral_angle_other_2_deg	0.092
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1320
Nucleic Acid Atoms	102
Solvent Atoms	167
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing