3A70 | pdb_00003a70

Crystal structure of Pseudomonas sp. MIS38 lipase in complex with diethyl phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZVD	PDB ENTRY 2ZVD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.1M Tris-HCl, pH8.5, 0.2M ammonium acetaet, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.297	α = 90
b = 104.297	β = 90
c = 496.182	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	ADSC QUANTUM 210	mirrors	2009-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	50	99.1	0.124	0.112	13.5	5.2		88120

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.23	100		0.378	0.376	3.44	4.9	8629

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 2ZVD	2.15	31.91	83034	4393	99.21	0.17273	0.17012	0.1704	0.22209	0.2204	RANDOM	21.854

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.876
r_dihedral_angle_4_deg	21.84
r_dihedral_angle_3_deg	14.384
r_dihedral_angle_1_deg	7.341
r_scangle_it	3.667
r_scbond_it	2.464
r_angle_refined_deg	1.878
r_mcangle_it	1.489
r_mcbond_it	0.879
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.116
r_metal_ion_refined	0.106
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9037
Nucleic Acid Atoms
Solvent Atoms	1121
Heterogen Atoms	66

Software

Software
Software Name	Purpose
BL38B1	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling