2WQ5

Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A3D	PDB ENTRY 1A3D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				26% PEG 4000, 0.24M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.712	α = 90
b = 68.712	β = 90
c = 68.712	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	RIGAKU CCD	MIRRORS	2008-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.65	34.4	100	0.09	10.6	10.8		13314		-3	23.9

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	1.65	1.71	99.9		0.53	2.1	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1A3D	1.65	34.36	12547	638	99.3	0.191	0.189	0.2	0.23	0.23	RANDOM	28.78

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.667
r_dihedral_angle_3_deg	13.963
r_dihedral_angle_4_deg	12.062
r_dihedral_angle_1_deg	6.749
r_scangle_it	2.517
r_scbond_it	1.837
r_angle_refined_deg	1.459
r_mcangle_it	1.264
r_angle_other_deg	0.905
r_mcbond_it	0.806
r_symmetry_vdw_refined	0.298
r_symmetry_hbond_refined	0.26
r_nbd_refined	0.257
r_mcbond_other	0.243
r_symmetry_vdw_other	0.205
r_nbtor_refined	0.194
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.092
r_nbtor_other	0.09
r_metal_ion_refined	0.02
r_symmetry_metal_ion_refined	0.018
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	925
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing