9H8I | pdb_00009h8i

Crystallization of B. licheniformis levanase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	10% w/v PEG 8000, 20% v/v ethylene glycol and 0.03 M Magnesium chloride, calcium chloride and 0.1 M bicine/Trizma base pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.586	α = 90
b = 82.586	β = 90
c = 171.088	γ = 90

Symmetry
Space Group	P 41 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	PIXEL	DECTRIS PILATUS 6M		2017-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	74.375	97.1	0.999	15.9	26.1		85690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57			0.698	0.639

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4fff	1.54	74.375	85314	4272	96.772	0.194	0.1928	0.204	0.2169	0.2288	23.445

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]
-0.132			-0.132		0.263

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.398
r_dihedral_angle_3_deg	12.529
r_lrange_it	8.627
r_lrange_other	8.626
r_dihedral_angle_1_deg	7.197
r_dihedral_angle_2_deg	6.503
r_scangle_it	6.481
r_scangle_other	6.48
r_scbond_it	4.193
r_scbond_other	4.192
r_mcangle_other	3.709
r_mcangle_it	3.705
r_mcbond_it	2.533
r_mcbond_other	2.509
r_angle_refined_deg	1.815
r_angle_other_deg	0.63
r_symmetry_nbd_refined	0.38
r_nbd_other	0.268
r_symmetry_nbd_other	0.199
r_nbd_refined	0.198
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.099
r_chiral_restr	0.094
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_symmetry_metal_ion_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_chiral_restr_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3583
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
MrBUMP	phasing
SCALA	data scaling