6CWL | pdb_00006cwl

Crystal structure of SpaA-SLH in complex with beta-D-GlcNAc-(1->3)-4,6-Pyr-beta-D-ManNAcOMe

X-RAY DIFFRACTION

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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	6.5	289	50 mM ammonium sulfate, 50 mM Bis-Tris, pH 6.5, 30% v/v pentaerythritolethoxylate [15/4 EO/OH]

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.256	α = 90
b = 72.256	β = 90
c = 126.14	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2014-10-08	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	2.15	40	99.9	0.073	0.076	0.021	11	13.2		21339

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	2.15	2.19	100		0.545	0.566	0.152	0.97		13.6	1068

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	2.15	40	20168	1132	99.82	0.2175	0.2154	0.2231	0.2552	0.2587	RANDOM	36.463

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]
0.04	0.02		0.04		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.85
r_dihedral_angle_3_deg	15.885
r_dihedral_angle_4_deg	12.469
r_dihedral_angle_1_deg	5.908
r_angle_refined_deg	1.581
r_mcangle_it	1.213
r_angle_other_deg	1.17
r_mcbond_it	0.687
r_mcbond_other	0.685
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2380
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	70

Software

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