1GQJ | pdb_00001gqj

Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with xylobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		NATIVE ALPHA-D-GLUCURONIDASE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8		30MG/ML, 15% PEG3350, 250MM MGCL2, 5MM TRIS PH8.0, 20% ETHYLENE GLYCOL 100MM XYLOTRIOSE, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.4	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.561	α = 115.23
b = 74.609	β = 93.15
c = 87.45	γ = 109.17

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MARRESEARCH	MSC/RIGAKU FOCUSSING MIRRORS	2001-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.9	20	95	0.089	9.4	2.5		109005

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	1.9	1.93	93.4		0.397	2.1	2.3

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	NATIVE ALPHA-D-GLUCURONIDASE	1.9	20	108150	830	94.7	0.173	0.172	0.18	0.221	0.22	RANDOM	17.64

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]
1.77	0.29	-0.25	-0.61	-1.02	-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.234
r_dihedral_angle_1_deg	4.528
r_scangle_it	3.054
r_scbond_it	2.016
r_angle_other_deg	1.771
r_angle_refined_deg	1.561
r_mcangle_it	1.222
r_mcbond_it	0.729
r_nbtor_other	0.456
r_nbd_refined	0.219
r_symmetry_vdw_other	0.196
r_nbd_other	0.189
r_symmetry_vdw_refined	0.18
r_chiral_restr	0.144
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.117
r_xyhbond_nbd_other	0.052
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11376
Nucleic Acid Atoms
Solvent Atoms	1383
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling