8XY5 | pdb_00008xy5

Open conformation of Burkholderia stagnalis lipase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LIP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	0.1 M HEPES, pH 7.0, 45% MPD, 1 M ammonium fluoride, 3% methanol

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.643	α = 90
b = 69.21	β = 98.531
c = 51.322	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	CCD	ADSC QUANTUM 270		2018-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.399	50	99.8	0.996	24.5	3.6		109236

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.399	1.42	99.9		0.835	0.627	1.8	3.4

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.399	29.243	109215	5565	99.666	0.163	0.163	0.162	0.162	0.1838	0.1838	14.617

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]
0.001			0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.559
r_dihedral_angle_3_deg	9.793
r_dihedral_angle_1_deg	6.122
r_dihedral_angle_2_deg	4.802
r_lrange_it	3.474
r_lrange_other	3.075
r_scangle_it	1.795
r_scangle_other	1.795
r_angle_refined_deg	1.19
r_scbond_it	1.12
r_scbond_other	1.119
r_mcangle_it	1.015
r_mcangle_other	1.015
r_mcbond_it	0.642
r_mcbond_other	0.642
r_angle_other_deg	0.441
r_nbd_other	0.228
r_nbd_refined	0.213
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.079
r_metal_ion_refined	0.076
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.006
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4682
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing