1NQ6 | pdb_00001nq6

Crystal Structure of the catalytic domain of xylanase A from Streptomyces halstedii JM8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E0W	PDB ENTRY 1E0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	PEG 4000, MAGNESIUM CHLORIDE, SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.61	22.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.05	α = 90
b = 79.6	β = 90
c = 87.8	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	120	IMAGE PLATE	MARRESEARCH		1996-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.885	EMBL/DESY, HAMBURG	BW7B

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	1.782	24.818	97.1	0.044	13.1		23589	22905			9.453

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	1.78	1.88	85.8		0.084	8.9

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	PDB ENTRY 1E0W	1.78	24.82	22865	21207	1658	96.73	0.1484	0.14745	0.14515	0.1473	0.17643	0.1789	RANDOM	13.257

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]
0.33			-0.8		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.029
r_scangle_it	1.95
r_scbond_it	1.245
r_angle_refined_deg	1.09
r_mcangle_it	0.717
r_mcbond_it	0.387
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing