4S24 | pdb_00004s24

1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	295	Protein: 10.2 mg/ml, 0.1M Tris HCl (pH 8.3), Screen: JSCG+ (C6), 0.1M Phosphate-citrate (pH 4.2), 40% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.046	α = 90
b = 72.046	β = 90
c = 166.766	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARMOSAIC 300 mm CCD	beryllium lenses	2014-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	30	99.9	0.067	0.067	62.5	15.2	29069	29069		-3	25.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	100		0.56	0.56	6.2	15.5	1417

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.7	29.41	27589	27589	1407	99.92	0.14937	0.14852	0.1485	0.16591	0.1652	RANDOM	33.702

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]
0.81	0.41		0.81		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.06
r_dihedral_angle_4_deg	18.773
r_dihedral_angle_3_deg	9.683
r_long_range_B_refined	7.212
r_long_range_B_other	6.98
r_scangle_other	3.992
r_dihedral_angle_1_deg	3.941
r_mcangle_it	2.784
r_mcangle_other	2.784
r_scbond_it	2.641
r_scbond_other	2.604
r_mcbond_it	1.795
r_mcbond_other	1.778
r_angle_refined_deg	1.432
r_angle_other_deg	0.812
r_chiral_restr	0.102
r_gen_planes_refined	0.022
r_gen_planes_other	0.017
r_bond_refined_d	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1531
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	45

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling