2ZUY | pdb_00002zuy

Crystal structure of exotype rhamnogalacturonan lyase YesX

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	7.1	293	20% PEG 3350, 0.2M Ammonium acetate, pH7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.853	α = 90
b = 88.07	β = 90
c = 99.304	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	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	1.000	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	1.65	50	98.9	0.094	8.2	9.8		77151

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)
	1.65	1.71	97.4		0.258	4.1	9.1

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 ENTRY 2Z8R	1.65	37.19	72362	3838	98.73	0.16177	0.16054	0.1599	0.18425	0.1846	RANDOM	10.801

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_2_deg	33.544
r_dihedral_angle_4_deg	17.444
r_dihedral_angle_3_deg	12.392
r_dihedral_angle_1_deg	5.995
r_scangle_it	1.93
r_scbond_it	1.261
r_angle_refined_deg	1.104
r_mcangle_it	0.806
r_mcbond_it	0.479
r_nbtor_refined	0.305
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.163
r_metal_ion_refined	0.146
r_symmetry_hbond_refined	0.101
r_xyhbond_nbd_refined	0.088
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4985
Nucleic Acid Atoms
Solvent Atoms	706
Heterogen Atoms	9

Software

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