1Z21 | pdb_00001z21

Crystal structure of the core domain of Yersinia pestis virulence factor YopR

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	291	17% PEG-8000, 85 mM Phosphate-citrate, 0.17 M NaCl, and 15% glycerol, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.662	α = 90
b = 85.662	β = 90
c = 85.662	γ = 90

Symmetry
Space Group	P 41 3 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	BRANDEIS		2003-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	1	NSLS	X9B

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	1.5	22.82	99.3	0.036	0.036	46.1	4.5	17699	17807	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.54	97.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIR	THROUGHOUT	1.499	22.81	2	17807	12054	640	71.36	0.2691	0.20526	0.20357	0.22	0.23833	0.26	RANDOM	21.596

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_1_deg	4.588
r_scangle_it	3.013
r_scbond_it	1.762
r_mcangle_it	1.285
r_angle_refined_deg	1.019
r_angle_other_deg	0.743
r_mcbond_it	0.667
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.25
r_nbd_other	0.222
r_xyhbond_nbd_refined	0.216
r_symmetry_hbond_refined	0.18
r_symmetry_vdw_other	0.177
r_nbtor_other	0.084
r_chiral_restr	0.057
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	771
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing