3QRY | pdb_00003qry

Analysis of a new family of widely distributed metal-independent alpha mannosidases provides unique insight into the processing of N-linked glycans, Streptococcus pneumoniae SP_2144 1-deoxymannojirimycin complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8		0.1 M Hepes, 1.2 M LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.46	α = 90
b = 158.8	β = 107.19
c = 60.04	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	117	CCD	MARMOSAIC 325 mm CCD		2010-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.75	158.8	99			88818	88818	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1.75	20	2	88818	88818	4679	97.4	0.17206	0.16959	0.17	0.21845	0.22	RANDOM	13.151

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]
1.74		0.63	-0.99		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	16.816
r_dihedral_angle_3_deg	12.927
r_dihedral_angle_1_deg	5.868
r_scangle_it	3.571
r_scbond_it	2.232
r_angle_refined_deg	1.401
r_mcangle_it	1.28
r_mcbond_it	0.748
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	16.816
r_dihedral_angle_3_deg	12.927
r_dihedral_angle_1_deg	5.868
r_scangle_it	3.571
r_scbond_it	2.232
r_angle_refined_deg	1.401
r_mcangle_it	1.28
r_mcbond_it	0.748
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6922
Nucleic Acid Atoms
Solvent Atoms	1388
Heterogen Atoms	46

Software

Software
Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
REFMAC	refinement
SCALA	data scaling

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.