5VKX

Coordination Chemistry within a Protein Host: Regulation of the Secondary Coordination Sphere

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	26 mg/mL protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.875	α = 90
b = 57.875	β = 90
c = 184.424	γ = 90

Symmetry
Space Group	I 41 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	PIXEL	DECTRIS PILATUS 6M		2016-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.37	37.4	99.5	22.2	11.1		33187

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.4	90.8			7.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.37	37.4	31548	1558	99.38	0.16481	0.16372	0.18737	RANDOM	20.589

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]
-0.1			-0.1		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.04
r_dihedral_angle_4_deg	14.626
r_dihedral_angle_3_deg	13.769
r_long_range_B_refined	10.656
r_long_range_B_other	10.652
r_dihedral_angle_1_deg	8.083
r_scangle_other	4.922
r_mcangle_other	3.618
r_mcangle_it	3.605
r_scbond_it	3.522
r_scbond_other	3.513
r_angle_refined_deg	2.866
r_mcbond_it	2.387
r_mcbond_other	2.377
r_angle_other_deg	2.06
r_chiral_restr	0.201
r_bond_refined_d	0.031
r_gen_planes_refined	0.016
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	924
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	46

Software

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