3F96 | pdb_00003f96

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

X-RAY DIFFRACTION

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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
2.47	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.078	α = 90
b = 82.455	β = 115.11
c = 96.586	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		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	2.1	50	96.1	0.083	11.22	3.6	45826	45826	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)
	2.1	2.18	73.1		0.264	1.9	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 (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	2.1	50	1	45826	43493	2325	95.67	0.20982	0.20626	0.2104	0.27766	RANDOM	36.515

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]
-1.45		-0.61	1.01		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.645
r_dihedral_angle_4_deg	20.376
r_dihedral_angle_3_deg	17.881
r_dihedral_angle_1_deg	7.381
r_scangle_it	4.218
r_scbond_it	2.91
r_mcangle_it	2.021
r_angle_refined_deg	1.896
r_mcbond_it	1.242
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.126
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6000
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms

Software

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