1LWB | pdb_00001lwb

Crystal structure of prokaryotic phospholipase A2 at atomic resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FAZ	PDB ENTRY 1FAZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	297	PEG 6000, lithium sulfate, sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.48	17.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.34	α = 90
b = 57.495	β = 111.07
c = 31.807	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	297	IMAGE PLATE	RIGAKU RAXIS IV		1997-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	0.71073

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	0.923	100	67.48	0.072	8.21	2.65		45532	2	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)
	0.923	0.954	22.75		0.228	1.64		1418

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB ENTRY 1FAZ	1.05	10	37649	37649	3423	82.2	0.1034	0.1034	0.1034		RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
34	844	1120.7

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.132
s_non_zero_chiral_vol	0.128
s_zero_chiral_vol	0.104
s_similar_adp_cmpnt	0.044
s_angle_d	0.035
s_anti_bump_dis_restr	0.035
s_from_restr_planes	0.0225
s_bond_d	0.022
s_rigid_bond_adp_cmpnt	0.01
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1852
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
X-PLOR	phasing