2ZE4

Crystal structure of phospholipase D from streptomyces antibioticus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	15% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.004	α = 90
b = 85.008	β = 90
c = 99.343	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	100	IMAGE PLATE	FUJI	mirrors	1997-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

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	2.5	100	90	0.056	14.1	2.9	19350	17415			26.2

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)
	2.5	2.59	78.6		0.151		2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	2.5	64.55	18600	15916	856	90.71	0.12374	0.12374	0.12111	0.17101	RANDOM	18.338

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]
-0.16			1.19		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.624
r_dihedral_angle_4_deg	24.565
r_dihedral_angle_3_deg	17.006
r_dihedral_angle_1_deg	7.078
r_scangle_it	5.296
r_scbond_it	3.159
r_mcangle_it	1.942
r_angle_refined_deg	1.917
r_mcbond_it	1.144
r_nbtor_refined	0.313
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.115
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3743
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Weissenberg	data collection
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing