3F97

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

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	6.6	293	PH 6.6, pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.47	48.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.084	α = 90
b = 82.697	β = 115.33
c = 96.692	γ = 90

Symmetry
Space Group	C 1 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	100	CCD	ADSC QUANTUM 315	ROSENBAUM-ROCK	2006-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9795	APS	24-ID-C

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	96.4	0.057	19.97	3.7	87071	87071	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	73.1		0.261	2.36	1.9

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	87071	82693	4376	96.2	0.18321	0.1817	0.21197	RANDOM	24.57

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]
-0.72		0.23	0.88		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.356
r_dihedral_angle_4_deg	14.257
r_dihedral_angle_3_deg	13.946
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.618
r_scbond_it	2.318
r_mcangle_it	1.552
r_angle_refined_deg	1.334
r_mcbond_it	0.915
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.356
r_dihedral_angle_4_deg	14.257
r_dihedral_angle_3_deg	13.946
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.618
r_scbond_it	2.318
r_mcangle_it	1.552
r_angle_refined_deg	1.334
r_mcbond_it	0.915
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.283
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6016
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	53

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 R01GM157729.