2GFF | pdb_00002gff

Crystal Structure of Yersinia pestis LsrG

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	20% PEG 6K, 100 mM MES, 0.17 M ammonium sulfate 100 microliter reservoir, 800 nanoliter drop,intelliplate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.174	α = 90
b = 56.174	β = 90
c = 119.397	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	70	CCD	ADSC QUANTUM 315		2005-07-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97910, 0.97951, 0.97444	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	50	99.3	0.077	11.4	8.5	20024	20024			29.1

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)
	1.75	1.81	98.9		0.68	0.68	1.9	6.4	1949

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 (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	MAD	THROUGHOUT	1.75	20	19884	18868	1016	99.37	0.20022	0.20022	0.19728	0.1974	0.25829	0.2603	RANDOM	30.581

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.983
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_3_deg	13.719
r_dihedral_angle_1_deg	5.497
r_scangle_it	4.943
r_scbond_it	3.573
r_mcangle_it	2.05
r_angle_refined_deg	1.714
r_mcbond_it	1.234
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.123
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
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	1593
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data scaling
SOLVE	phasing