7CRE | pdb_00007cre

hnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLOIN element

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	25 % w/v Polyethylene glycol 3350, 100 mM BIS-TRIS pH 5.5, 200 mM Ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.611	α = 90
b = 61.611	β = 90
c = 144.544	γ = 120

Symmetry
Space Group	P 62 2 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	CCD	MARMOSAIC 325 mm CCD		2019-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9792	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3	50	98.8	0.151	0.159	0.049	13.7	11.5		3670

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	100		0.889	0.324		11.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ZZI	3	20	3239	365	98.6	0.26	0.2579	0.2632	0.2792	0.2893	RANDOM	142.491

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]
-9.41	-4.71		-9.41		30.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.54
r_dihedral_angle_3_deg	18.431
r_rigid_bond_restr	17.827
r_dihedral_angle_4_deg	9.805
r_dihedral_angle_1_deg	7.553
r_angle_other_deg	1.992
r_angle_refined_deg	1.156
r_chiral_restr	0.044
r_bond_other_d	0.027
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	546
Nucleic Acid Atoms	159
Solvent Atoms	11
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing