3F9C | pdb_00003f9c

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

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. NATIVE PROTEIN CRYSTAL SOAKED IN MOTHER LIQUOR CONTAINING DFP, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.47	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.375	α = 90
b = 82.4	β = 115.64
c = 96.511	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	IMAGE PLATE	RIGAKU	OSMIC BLUE	2008-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.3	50	100	0.069	20.71	4.2	36675	36675	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)
	2.3	2.38	100		0.44	3.23	4.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	NATIVE STRUCTURE, PDB ENTRY 3D59	2.3	50	1	36675	34789	1826	99.94	0.19919	0.19595	0.2	0.26109	RANDOM	36.908

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]
-1.48		0.46	0.56		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	20.355
r_dihedral_angle_3_deg	17.355
r_dihedral_angle_1_deg	7.823
r_scangle_it	3.825
r_scbond_it	2.59
r_angle_refined_deg	1.813
r_mcangle_it	1.752
r_mcbond_it	1.058
r_symmetry_vdw_refined	0.352

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	20.355
r_dihedral_angle_3_deg	17.355
r_dihedral_angle_1_deg	7.823
r_scangle_it	3.825
r_scbond_it	2.59
r_angle_refined_deg	1.813
r_mcangle_it	1.752
r_mcbond_it	1.058
r_symmetry_vdw_refined	0.352
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.291
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5978
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	20

Software

Software
Software Name	Purpose
StructureStudio	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.