5UB6 | pdb_00005ub6

XAC2383 from Xanthomonas citri bound to pyrophosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	20 mM Tris pH 8.0, 300 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2	38.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.544	α = 90
b = 66.86	β = 90
c = 113.033	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2014-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	43.69	98.51	8.73	4.7		24778

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.2	43.69	24778	1351	97.63	0.16797	0.16463	0.17	0.229	0.22	RANDOM	31.096

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]
-0.15			0.18		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	18.974
r_dihedral_angle_3_deg	14.642
r_dihedral_angle_1_deg	6.589
r_long_range_B_refined	6.226
r_long_range_B_other	6.175
r_scangle_other	4.599
r_mcangle_it	3.094
r_mcangle_other	3.093
r_scbond_it	2.96
r_scbond_other	2.934
r_mcbond_it	2.088
r_mcbond_other	2.084
r_angle_refined_deg	1.73
r_angle_other_deg	1.005
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4382
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	18

Software

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