4PUD | pdb_00004pud

Extracellulr Xylanase from Geobacillus stearothermophilus: E159Q mutant, with xylopentaose in active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R86

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	293	16% PEG 4000, 0.1M MES, 10mM Zinc chloride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.394	α = 90
b = 61.664	β = 119.37
c = 89.321	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS HTC		2013-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.01	50	98.99	0.098		5.7	36157	36157

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01		94.54

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1R86	2.01	50	36157	36157	1901	98.99	0.14815	0.14815	0.14631	0.1579	0.18342	0.1938	RANDOM	31.834

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]
0.98		-0.54	1.37		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.061
r_dihedral_angle_4_deg	15.574
r_dihedral_angle_3_deg	15.21
r_dihedral_angle_1_deg	6.551
r_angle_refined_deg	2.029
r_angle_other_deg	0.928
r_chiral_restr	0.129
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	58

Software

Software
Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement
HKL-3000	data reduction
SCALA	data scaling
REFMAC	phasing