6JNL | pdb_00006jnl

REF6 ZnF2-4-NAC004 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R2S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	12% PEG 3,350, 0.2 M NH4F

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.16	α = 90
b = 89.16	β = 90
c = 72.603	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS3 S 6M		2016-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	30	99.9	0.053	52.16	17.7		18924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12			0.59

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	4R2S	2.15	30	15643	810	99.84	0.20701	0.20488	0.22	0.24923	0.26	RANDOM	65.583

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]
0.53			0.53		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.889
r_dihedral_angle_4_deg	24.087
r_dihedral_angle_3_deg	19.334
r_long_range_B_other	9.536
r_long_range_B_refined	9.529
r_scangle_other	7.871
r_dihedral_angle_1_deg	7.388
r_mcangle_it	7.172
r_mcangle_other	7.168
r_scbond_it	6.142
r_scbond_other	6.122
r_mcbond_it	5.633
r_mcbond_other	5.632
r_angle_refined_deg	1.963
r_angle_other_deg	1.468
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	739
Nucleic Acid Atoms	465
Solvent Atoms	24
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing