2VGD | pdb_00002vgd

Crystal structure of environmental isolated GH11 in complex with xylobiose and feruloyl-arabino-xylotriose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		APO FORM OF ENXYN11A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.6		3.75 MM FAX3 0.2 M AMMONIUM FORMATE, PH 6.6 AND 17% (W/V) POLYETHYLENE GLYCOL 3350

Crystal Properties
Matthews coefficient	Solvent content
3.2	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.47	α = 90
b = 76.47	β = 90
c = 102.6	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2005-04-01	M	SINGLE WAVELENGTH

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

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	1.8	31	99.8	0.09	20.8	6.8		27316		2

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	1.79	1.89	99.6		0.75	2	6.8

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	APO FORM OF ENXYN11A	1.8	30.66	27316	1460	99.8	0.177	0.175	0.17	0.203	0.2	RANDOM	18.89

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.377
r_dihedral_angle_4_deg	20.762
r_dihedral_angle_3_deg	11.227
r_dihedral_angle_1_deg	7.63
r_scangle_it	2.845
r_scbond_it	1.902
r_angle_refined_deg	1.431
r_mcangle_it	1.161
r_mcbond_it	0.662
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
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_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	1505
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing