6YZD | pdb_00006yzd

Crystal structure of the M295A 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
2.05	39.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.44	α = 90
b = 104.1	β = 90
c = 163.13	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		2019-05-26	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	1.41	30.36	99.9	0.999	13	6.7		168970

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	1.41	1.43			0.621

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4M3H	1.41	30.36	168969	8343	99.828	0.201	0.1998	0.21	0.2249	0.23	21.936

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]
-1.758			-0.835		2.593

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.611
r_dihedral_angle_4_deg	14.774
r_dihedral_angle_3_deg	12.425
r_dihedral_angle_1_deg	7.385
r_lrange_it	4.585
r_lrange_other	4.584
r_scangle_it	3.547
r_scangle_other	3.524
r_mcangle_it	2.595
r_mcangle_other	2.595
r_scbond_it	2.414
r_scbond_other	2.401
r_mcbond_it	1.899
r_mcbond_other	1.894
r_angle_refined_deg	1.657
r_angle_other_deg	1.482
r_symmetry_nbd_refined	0.201
r_nbd_refined	0.197
r_symmetry_nbd_other	0.193
r_nbd_other	0.187
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.142
r_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.076
r_metal_ion_refined	0.07
r_symmetry_xyhbond_nbd_other	0.059
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	6286
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing