3F98

Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by tabun

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D59	NATIVE STRUCTURE, PDB ENTRY 3D59

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.984	α = 90
b = 133.322	β = 90
c = 253.855	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315	ROSENBAUM-ROCK	2006-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0055	APS	19-ID

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	1.7	50	98.8	0.07	35.025	10	141507	141507	1	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)
	1.7	1.76	97.8		0.435	5.59	10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	NATIVE STRUCTURE, PDB ENTRY 3D59	1.7	50	1	141507	134355	7097	98.81	0.18008	0.17894	0.20165	RANDOM	20.122

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]
0.05			0.04		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.83
r_dihedral_angle_4_deg	16.931
r_dihedral_angle_3_deg	14.629
r_dihedral_angle_1_deg	6.5
r_scangle_it	2.945
r_scbond_it	1.941
r_mcangle_it	1.456
r_angle_refined_deg	1.349
r_mcbond_it	0.887
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.83
r_dihedral_angle_4_deg	16.931
r_dihedral_angle_3_deg	14.629
r_dihedral_angle_1_deg	6.5
r_scangle_it	2.945
r_scbond_it	1.941
r_mcangle_it	1.456
r_angle_refined_deg	1.349
r_mcbond_it	0.887
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9351
Nucleic Acid Atoms
Solvent Atoms	1342
Heterogen Atoms	24

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

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 R01GM133198.