4E4P | pdb_00004e4p

Second native structure of Xylanase A1 from Paenibacillus sp. JDR-2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294.5	200 mM MgCl2, 100mM HEPES sodium salt, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.518	α = 90
b = 58.528	β = 108.81
c = 65.024	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	105	CCD	MARMOSAIC 325 mm CCD			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	1.92	84.82	99.9	0.109	3.9	7.4		48561		2

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	1.92	2	100			7	4845

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	1.92	50	48381	2440	98.69	0.2555	0.2534	0.2692	0.2946	0.3027	RANDOM	44.588

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]
0.81		1.24	-1.81		1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.328
r_dihedral_angle_3_deg	16.408
r_dihedral_angle_4_deg	13.058
r_dihedral_angle_1_deg	6.351
r_scangle_it	5.378
r_scbond_it	3.525
r_mcangle_it	1.911
r_angle_refined_deg	1.903
r_mcbond_it	1.13
r_chiral_restr	0.141
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4644
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction