3DT8 | pdb_00003dt8

Crystal Structure of Bovin Brain 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	1WAB	PDB ENTRY 1WAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.322	α = 90
b = 81.322	β = 90
c = 72.784	γ = 120

Symmetry
Space Group	P 31 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	2003-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	1.85	70.36	96.1	0.051	26.52	5.8	23181	23181	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)
	1.85	1.92	98.2		0.577	1.2	5.4

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	PDB ENTRY 1WAB	1.85	30	1	21079	21079	1157	92.2	0.20535	0.20399	0.2	0.2307	RANDOM	24.879

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]
-0.34	-0.17		-0.34		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.27
r_dihedral_angle_4_deg	18.858
r_dihedral_angle_3_deg	15.988
r_dihedral_angle_1_deg	5.597
r_scangle_it	4.191
r_scbond_it	2.621
r_mcangle_it	1.778
r_mcbond_it	1.484
r_angle_refined_deg	1.443
r_nbtor_refined	0.311
r_nbd_refined	0.223
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.107
r_symmetry_hbond_refined	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1696
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
REFMAC	phasing