3RDK | pdb_00003rdk

Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	294.5	Protein to mother liquor at 2:1 ratio. mother liquor, 18% PEG 3350, 100mM HEPES, 200mM MgCl2, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.113	α = 90
b = 165.113	β = 90
c = 66.355	γ = 90

Symmetry
Space Group	P 43 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	105	CCD	MARMOSAIC 325 mm CCD		2009-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979	SSRL	BL12-2

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	1.49	117.04		0.047	33.7	8.8	149014	148538

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.49	117.04	140983	7447	99.67	0.1472	0.14523	0.15	0.18415	0.19	RANDOM	30.787

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]
0.75			0.75		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.002
r_dihedral_angle_3_deg	13.92
r_dihedral_angle_4_deg	12.646
r_scangle_it	7.428
r_dihedral_angle_1_deg	6.963
r_scbond_it	5.479
r_mcangle_it	3.612
r_rigid_bond_restr	3.164
r_mcbond_it	2.652
r_angle_refined_deg	2.321
r_chiral_restr	0.188
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5300
Nucleic Acid Atoms
Solvent Atoms	720
Heterogen Atoms	140

Software

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