3A6Z

Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation following dialysis against Ca-free buffer

X-RAY DIFFRACTION

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 acetate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.382	α = 90
b = 104.382	β = 90
c = 495.175	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	Bruker DIP-6040	mirrors	2009-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.0	SPring-8	BL44XU

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	99.3	0.136	0.109	13.76	6.9		87709

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)
	2.15	2.23	99.2		0.437	3.1	5.6	8579

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZVD	2.15	48.11	83266	4397	99.45	0.18431	0.18244	0.21965	RANDOM	21.34

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.304
r_dihedral_angle_4_deg	22.138
r_dihedral_angle_3_deg	15.402
r_dihedral_angle_1_deg	7.276
r_scangle_it	3.61
r_scbond_it	2.542
r_angle_refined_deg	1.724
r_mcangle_it	1.573
r_mcbond_it	0.977
r_symmetry_hbond_refined	0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.304
r_dihedral_angle_4_deg	22.138
r_dihedral_angle_3_deg	15.402
r_dihedral_angle_1_deg	7.276
r_scangle_it	3.61
r_scbond_it	2.542
r_angle_refined_deg	1.724
r_mcangle_it	1.573
r_mcbond_it	0.977
r_symmetry_hbond_refined	0.51
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.122
r_metal_ion_refined	0.099
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9078
Nucleic Acid Atoms
Solvent Atoms	631
Heterogen Atoms	17

Software

Software
Software Name	Purpose
BL44XU	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.