4C1S | pdb_00004c1s

Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroides thetaiotaomicron VPI-5482

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K7X	PDB ENTRY 3K7X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 MONOMETHYL ETHER, 0.25 M SODIUM ACETATE, AND BIS-TRIS-HCL (PH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.1	α = 90
b = 44.42	β = 101.43
c = 103.05	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	MARRESEARCH MX-300HE	COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT)	2012-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

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	2.1	48	99.9	0.11	10.4	4.2		52497

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	2.1	2.21	99.9		0.48	3.3	4.2

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 3K7X	2.1	48.03	49817	2674	99.83	0.2156	0.21359	0.2	0.25264	0.23	RANDOM	24.111

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]
12.47		-21.1	-13.73		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.243
r_dihedral_angle_4_deg	19.648
r_dihedral_angle_3_deg	15.706
r_dihedral_angle_1_deg	7.162
r_mcangle_it	3.252
r_scbond_it	3.071
r_mcbond_it	2.425
r_angle_refined_deg	1.597
r_chiral_restr	0.117
r_bond_refined_d	0.014
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6078
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
AutoProcess	data reduction
SCALA	data scaling
PHASER	phasing