4AHS | pdb_00004ahs

Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BI4	PDB ENTRY 1BI4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION.

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.183	α = 90
b = 71.183	β = 90
c = 66.653	γ = 120

Symmetry
Space Group	P 31

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 210r		2008-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1		Australian Synchrotron	MX1

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	1.75	61.7	96.5	0.07	16.2	4.9		36824		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	1.75	1.84	80.9		0.45	1.9	2.6

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 1BI4	1.75	61.66	34485	1841	95.29	0.20763	0.20553	0.2	0.24787	0.24	RANDOM	25.24

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]
0.25	0.13		0.25		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.922
r_dihedral_angle_4_deg	18.621
r_dihedral_angle_3_deg	16.665
r_dihedral_angle_1_deg	6.36
r_angle_refined_deg	2.242
r_chiral_restr	0.144
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	2336
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing