5NBS | pdb_00005nbs

Structural studies of a Glycoside Hydrolase Family 3 beta-glucosidase from the Model Fungus Neurospora crassa

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	293	0.2 M ammonium citrate dibasic at pH 5.1 and 20 % w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
5.1	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.931	α = 90
b = 286.837	β = 90
c = 58.045	γ = 90

Symmetry
Space Group	P 21 21 2

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 225 mm CCD		2013-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	47	99.2	0.028	0.04	0.028	0.998	22.9	1.9		113592			29.7

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	2.308	99.15		0.38	0.53	0.38	0.825	4.3	1.9

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	4IIB	2.25	47	107929	5627	99.17	0.18227	0.18035	0.19	0.21968	0.22	RANDOM	34.929

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]
-3.61			0.78		2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.475
r_dihedral_angle_4_deg	16.858
r_dihedral_angle_3_deg	13.439
r_dihedral_angle_1_deg	5.604
r_long_range_B_refined	4.049
r_long_range_B_other	3.945
r_angle_refined_deg	1.357
r_scangle_other	0.931
r_angle_other_deg	0.92
r_mcangle_it	0.755
r_mcangle_other	0.755
r_scbond_it	0.51
r_scbond_other	0.51
r_mcbond_it	0.413
r_mcbond_other	0.413
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12988
Nucleic Acid Atoms
Solvent Atoms	954
Heterogen Atoms	1021

Software

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