3GZA | pdb_00003gza

Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	277	0.200M sodium citrate, 20.00% PEG-3350, No Buffer pH 8.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.052	α = 90
b = 81.532	β = 103.55
c = 111.572	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-02-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97828,0.97916	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	28.072	99.7	0.074	0.074	6.547	3		133836			16.908

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	100		0.365	0.365	2	2.9	9900

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	MAD	THROUGHOUT	1.6	28.072	133835	6726	99.65	0.14	0.139	0.15	0.168	0.18	RANDOM	28.212

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]
0.24		-1.1	0.35		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.928
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_3_deg	10.606
r_dihedral_angle_1_deg	4.657
r_scangle_it	3.155
r_scbond_it	2.101
r_angle_refined_deg	1.738
r_mcangle_it	1.291
r_angle_other_deg	1.283
r_mcbond_it	0.803
r_mcbond_other	0.266
r_symmetry_hbond_refined	0.237
r_symmetry_vdw_other	0.213
r_nbd_refined	0.211
r_nbd_other	0.197
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.184
r_metal_ion_refined	0.131
r_chiral_restr	0.11
r_nbtor_other	0.093
r_symmetry_vdw_refined	0.078
r_xyhbond_nbd_other	0.046
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6906
Nucleic Acid Atoms
Solvent Atoms	1234
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction