3P2C | pdb_00003p2c

Crystal structure of an exo-alpha-1,6-mannosidase (bacova_03347) from bacteroides ovatus at 1.60 a resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	20.00% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.722	α = 90
b = 89.854	β = 105.61
c = 90.387	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	100	CCD	MARMOSAIC 325 mm CCD		2010-05-13	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.6	29.521	99	0.068	10.65			130811		-3	17.675

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	97.9		0.725	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.6	29.521	130777	6582	99.72	0.1356	0.1339	0.15	0.1682	0.18	RANDOM	24.506

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]
-1.38		-0.82	0.78		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.26
r_dihedral_angle_4_deg	18.245
r_dihedral_angle_3_deg	11.942
r_dihedral_angle_1_deg	5.947
r_scangle_it	4.847
r_scbond_it	3.565
r_mcangle_it	2.292
r_mcbond_it	1.626
r_angle_refined_deg	1.534
r_angle_other_deg	0.965

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.26
r_dihedral_angle_4_deg	18.245
r_dihedral_angle_3_deg	11.942
r_dihedral_angle_1_deg	5.947
r_scangle_it	4.847
r_scbond_it	3.565
r_mcangle_it	2.292
r_mcbond_it	1.626
r_angle_refined_deg	1.534
r_angle_other_deg	0.965
r_mcbond_other	0.54
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7128
Nucleic Acid Atoms
Solvent Atoms	1150
Heterogen Atoms	62

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.