7SV3 | pdb_00007sv3

Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAcOMe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CWM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291.15	0.1 M sodium acetate trihydrate pH 4.5, 2.0 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.652	α = 90
b = 67.916	β = 90
c = 72.905	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 200K		2018-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.7	20	100	0.145	0.154	0.048	11.8	7.9		19791

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	99.9		0.773	0.859	0.369	0.774		5.2

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6CWM	1.7	19.9	18483	1062	99.65	0.1856	0.184	0.2129	0.2371	RANDOM	15.054

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]
-0.16			0.79		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.717
r_dihedral_angle_3_deg	11.279
r_dihedral_angle_4_deg	10.718
r_dihedral_angle_1_deg	5.245
r_angle_other_deg	1.301
r_angle_refined_deg	1.246
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1306
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	35

Software

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