6YZF

Crystal structure of the M295Y variant of Ssl1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50 mM HEPES pH 7.0, 1.4 M ammonium sulfate, 10 mM [Co(NH3)6]Cl3

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 104.24	β = 90
c = 162.06	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0	PETRA III, DESY	P11

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	1.68	49.043	99.3	0.997	8.87	1.9		98807

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	1.684	1.692			0.572

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	4M3H	1.684	49.043	98712	4943	99.271	0.193	0.1906	0.232	25.32

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]
-1.875			0.048		1.826

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	35.009
r_dihedral_angle_2_deg	28.806
r_dihedral_angle_4_deg	16.178
r_dihedral_angle_3_deg	13.393
r_dihedral_angle_1_deg	7.561
r_lrange_it	6.15
r_lrange_other	6.149
r_scangle_it	4.097
r_scangle_other	4.064
r_mcangle_it	3.383
r_mcangle_other	3.383
r_scbond_it	2.952
r_scbond_other	2.902
r_mcbond_it	2.272
r_mcbond_other	2.272
r_angle_refined_deg	1.628
r_angle_other_deg	1.402
r_metal_ion_refined	0.226
r_nbd_refined	0.195
r_symmetry_nbd_other	0.191
r_nbd_other	0.186
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.144
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.078
r_symmetry_metal_ion_refined	0.027
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6250
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	25

Software

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