Experiment: 1QD6

OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QD5	MONOMER OMPLA (1QD5) WITHOUT WATER/DETERGENT MOLECULES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293	PEG400, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.067	α = 90
b = 84.038	β = 90
c = 95.245	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		1998-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID2		ESRF	ID2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	20.3	74.1	0.077	10.9	2.69	76223	28336			27.1

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)
1	2.1	2.17	66.7		0.265			2510

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	MONOMER OMPLA (1QD5) WITHOUT WATER/DETERGENT MOLECULES	2.1	20.3	28947	2408	74.1	0.226	0.226	0.283	RANDOM	34.5

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]
-0.78			0.13		0.65

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	27.2
x_scangle_it	7.28
x_scbond_it	5.85
x_mcangle_it	3.28
x_mcbond_it	2.4
x_angle_deg	1.2
x_improper_angle_d	1.08
x_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4111
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	42

Software

Software
Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling