6CWR | pdb_00006cwr

Crystal structure of SpaA-SLH/G46A/G109A in complex with 4,6-Pyr-beta-D-ManNAcOMe

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1 M Bis-Tris, pH 6.5, 28% PEG2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.13	36.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.543	α = 90
b = 65.834	β = 90
c = 71.919	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	289	CCD	MARMOSAIC 300 mm CCD		2016-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

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	1.24	30	99.2	0.04	0.045	0.02	16.1	4.1		44339

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	1.24	1.28	97.3		0.693	0.844	0.473	0.66		2.8	3548

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	PDB entry 6CWC	1.24	30	42050	2218	98.91	0.1483	0.1466	0.15	0.1789	0.18	RANDOM	18.404

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]
1.25			0.01		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.592
r_sphericity_free	20.465
r_dihedral_angle_4_deg	13.383
r_dihedral_angle_3_deg	12.183
r_sphericity_bonded	8.726
r_dihedral_angle_1_deg	5.084
r_rigid_bond_restr	1.787
r_mcangle_it	1.726
r_angle_refined_deg	1.481
r_mcbond_it	1.381

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.592
r_sphericity_free	20.465
r_dihedral_angle_4_deg	13.383
r_dihedral_angle_3_deg	12.183
r_sphericity_bonded	8.726
r_dihedral_angle_1_deg	5.084
r_rigid_bond_restr	1.787
r_mcangle_it	1.726
r_angle_refined_deg	1.481
r_mcbond_it	1.381
r_mcbond_other	1.376
r_angle_other_deg	0.932
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1276
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	21

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.