2ZUX

Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z8R	PDB ENTRY 2Z8R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	293	55% MPD, 0.1M TRIS, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.282	α = 90
b = 105.858	β = 94.82
c = 100.967	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU JUPITER 210	mirror	2008-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.8000	SPring-8	BL38B1

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	1.32	50	97.6	0.066	13	3.8		280440

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)
	1.32	1.37	95.1		0.338	2.8	3.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Z8R	1.32	50	259908	13803	97.39	0.16704	0.16633	0.18033	RANDOM	16.536

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]
0.1		0.52	0.74		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.316
r_dihedral_angle_4_deg	17.449
r_dihedral_angle_3_deg	11.393
r_dihedral_angle_1_deg	6.497
r_scangle_it	1.915
r_scbond_it	1.326
r_angle_refined_deg	1.166
r_mcangle_it	0.882
r_mcbond_it	0.547
r_nbtor_refined	0.307
r_nbd_refined	0.197
r_metal_ion_refined	0.153
r_symmetry_vdw_refined	0.137
r_symmetry_hbond_refined	0.106
r_chiral_restr	0.079
r_xyhbond_nbd_refined	0.077
r_symmetry_metal_ion_refined	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8954
Nucleic Acid Atoms
Solvent Atoms	1271
Heterogen Atoms	97

Software

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