9HTS | pdb_00009hts

Human KHNYN KH domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	100 mM Tris, 250 mM NaCl, 35 % PEG 3000, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.833	α = 90
b = 121.797	β = 108.545
c = 44.547	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 16M		2021-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.198	60.899	73.3	0.995	7.5	5.4		10852

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	2.2	2.26			0.577

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.198	60.899	10852	780	73.3	0.201	0.1961	0.2015	0.2585	0.2567	RANDOM	31.986

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]
-0.175		0.137	0.048		0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.014
r_dihedral_angle_6_deg	14.472
r_dihedral_angle_2_deg	9.497
r_lrange_it	7.659
r_lrange_other	7.659
r_dihedral_angle_1_deg	6.07
r_scangle_it	5.464
r_scangle_other	5.462
r_mcangle_it	3.946
r_mcangle_other	3.945
r_scbond_it	3.335
r_scbond_other	3.334
r_mcbond_it	2.489
r_mcbond_other	2.489
r_angle_refined_deg	1.414
r_angle_other_deg	0.472
r_nbd_other	0.242
r_nbd_refined	0.224
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_other	0.136
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.125
r_ncsr_local_group_1	0.113
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing