5A6V | pdb_00005a6v

Open and closed conformations and protonation states of Candida antarctica Lipase B: Xenon complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TCA	PDB ENTRY 1TCA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	CANDIDA ANTARCTICA LIPASE B (CALB) WAS PURCHASED BY HAMPTON RESEARCH AND CRYSTALLIZED WITHOUT FURTHER PURIFICATION. CRYSTALLIZATION TRIALS WERE PERFORMED AT 293 K USING THE HANGING-DROP METHOD USING A QUIAGEN EASYXTAL 15-WELL PLATE. 1 UL OF A 15 MG/ML CALB SOLUTION IN 20MM NA(CH3COO) PH = 4.8 WAS DILUTED WITH 1 UL OF THE PRECIPITANT SOLUTION, MADE OF 200MM NA(CH3COO) PH = 4.8, 20% (W/V) PEG4000, AND 10-13% (V/V) 2-PROPANOL. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION AGAINST 500 ML OF THE PRECIPITANT SOLUTION. PROTEIN CRYSTALS OF NATIVE CALB APPEARED WITHIN ONE WEEK AND GREW TO A SIZE OF 0.2 X 0.4 X 0.5 MM3 IN THREE WEEKS

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.656	α = 87.8
b = 48.89	β = 98.07
c = 71.68	γ = 108.17

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M	KB MIRRORS	2013-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)		PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.27	70.96	92.7	0.06	29.5	6.2		21330		7

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	2.27	2.36	70.5		0.34	7.2	4.6

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 1TCA	2.28	70.97	20233	1097	92.18	0.14226	0.1393	0.14	0.1948	0.19	RANDOM	14.381

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]
0.05	0.17	-0.11	0.01	-0.2	-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.209
r_dihedral_angle_4_deg	18.545
r_dihedral_angle_3_deg	13.606
r_dihedral_angle_1_deg	6.235
r_scbond_it	1.585
r_mcangle_it	1.53
r_angle_refined_deg	1.416
r_mcbond_it	1.021
r_chiral_restr	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
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	4639
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing