5A71 | pdb_00005a71

Open and closed conformations and protonation states of Candida antarctica Lipase B: atomic resolution native

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 = 39.67	α = 88.74
b = 48.94	β = 97.15
c = 71.61	γ = 108.44

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	2013-03-21	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	0.91	71.04	94.5	0.11	13.65	17.2		343684		1.5

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	0.91	0.93	77.4		0.57	1.59	3.5

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	0.91	71.04	326301	17383	94.48	0.11255	0.1115	0.13	0.13197	0.14	RANDOM	11.793

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]
-0.04	-0.23	-0.1	0.4	0.16	-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.794
r_dihedral_angle_2_deg	33.317
r_dihedral_angle_4_deg	20.037
r_dihedral_angle_3_deg	11.303
r_sphericity_bonded	11.239
r_rigid_bond_restr	6.779
r_dihedral_angle_1_deg	6.583
r_angle_refined_deg	2.257
r_scbond_it	2.177
r_mcangle_it	1.565
r_angle_other_deg	1.454
r_mcbond_it	1.324
r_mcbond_other	1.321
r_chiral_restr	0.159
r_bond_refined_d	0.026
r_gen_planes_refined	0.013
r_gen_planes_other	0.009
r_bond_other_d	0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4632
Nucleic Acid Atoms
Solvent Atoms	1019
Heterogen Atoms	77

Software

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