6Z3N | pdb_00006z3n

Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	12 mg/mL of PaSpo2 protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, and 10 mM MgCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M NH4OAc, 0.1 M Bis-Tris propane, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.31	α = 90
b = 85.9	β = 102.34
c = 122.64	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 XE 16M		2019-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.58	59.9	81.3	0.999	23.2	5.9		95945

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.61			0.573

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	1.58	59.9	95945	4868	81.169	0.141	0.1374	0.1398	0.2004	0.2013	33.78

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]
-0.32		-1.978	2.023		-0.764

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.559
r_dihedral_angle_4_deg	20.675
r_dihedral_angle_3_deg	14.962
r_scangle_other	8.996
r_scangle_it	8.995
r_lrange_it	8.442
r_lrange_other	8.348
r_scbond_it	7.615
r_scbond_other	7.615
r_mcangle_it	6.858
r_mcangle_other	6.857
r_dihedral_angle_1_deg	6.392
r_mcbond_it	5.961
r_mcbond_other	5.961
r_rigid_bond_restr	3.864
r_angle_refined_deg	1.676
r_angle_other_deg	1.513
r_nbd_refined	0.223
r_nbd_other	0.197
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_nbd_refined	0.154
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5632
Nucleic Acid Atoms
Solvent Atoms	566
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
CRANK2	phasing