3I6B | pdb_00003i6b

Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R8E	PDB CODE: 2R8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	294	1.875 M Ammonium Sulfate, 100mM Na Cacodylate pH 6.5, 2.5% glycerol, stoichiometric amount of Kdo8P (cleaved upon incubation in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.964	α = 90
b = 144.104	β = 90
c = 145.854	γ = 90

Symmetry
Space Group	C 2 2 21

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		2007-12-06

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

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	2.49	50	92.7	0.125	8.9	4.1		21494		2.3

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	2.49	2.65	94.2		0.46	2.3	3.9

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 CODE: 2R8E	2.49	40	21494	1132	92.7	0.202	0.2	0.2	0.238	0.24	RANDOM	24.34

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]
-1			-0.17		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.421
r_dihedral_angle_4_deg	17.965
r_dihedral_angle_3_deg	14.727
r_dihedral_angle_1_deg	4.855
r_scangle_it	1.799
r_scbond_it	1.137
r_angle_refined_deg	1.072
r_mcangle_it	0.633
r_mcbond_it	0.491
r_nbtor_refined	0.298
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	5198
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	56

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling