1ILD | pdb_00001ild

OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE SITE MUTANT pH 4.6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QD5	1QD5 MUTATED ACTIVE SITE RESIDUES to ALA AND GAVE ALL ATOMS A RANDOM SHIFT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	MPD, calcium chloride, Bis-Tris buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.484	α = 90
b = 78.484	β = 90
c = 101.669	γ = 120

Symmetry
Space Group	P 31 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	120	IMAGE PLATE	MAC Science DIP-2000	mirrors	1999-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	2.8	20	99.3	0.064	0.064	25.4	10		9276		-3

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)
	2.8	2.85	99.6		0.343	0.343	4.9		453

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1QD5 MUTATED ACTIVE SITE RESIDUES to ALA AND GAVE ALL ATOMS A RANDOM SHIFT	2.8	20	9276	9231	900	99.2	0.211	0.2	0.275	0.26	SAME AS SET USED IN REFINEMENT OF THE NATIVE STRUCTURE (1QD5). FROM THE ADDITIONAL REFLECTIONS 10% WAS RANDOMLY SELECTED FOR THE TEST SET

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]
-7.449	-12.686		-7.449		14.899

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.6
c_angle_deg	1.5
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2091
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	100

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	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.