6CWF | pdb_00006cwf

Crystal structure of SpaA-SLH in complex with 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 calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72	α = 90
b = 72	β = 90
c = 125.567	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	IMAGE PLATE	RIGAKU RAXIS	OSMIC BLUE MIRRORS	2014-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002+	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	2.25	40	100	0.047	0.05	0.016	14.5	9.4		18478

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	2.25	2.29	100		0.653	0.691	0.222	0.871		9.5

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	2.25	40	17170	920	97.79	0.2143	0.2122	0.2175	0.2535	0.2523	RANDOM	43.086

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]
-0.11	-0.05		-0.11		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.398
r_dihedral_angle_3_deg	17.311
r_dihedral_angle_4_deg	12.667
r_dihedral_angle_1_deg	5.78
r_mcangle_it	1.689
r_angle_refined_deg	1.678
r_angle_other_deg	1.16
r_mcbond_other	0.987
r_mcbond_it	0.986
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2540
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	42

Software

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