7DFM | pdb_00007dfm

Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	293	2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.039	α = 90
b = 135.039	β = 90
c = 72.343	γ = 120

Symmetry
Space Group	P 32 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	95	PIXEL	DECTRIS PILATUS3 2M		2018-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.4	100	100	0.225	10.8	19.3		30040

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	2.4	2.49			1.23	1.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1HIX	2.4	49.409	30003	1571	99.983	0.172	0.1678	0.17	0.2449	0.25	26.848

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]
-0.013	-0.006		-0.013		0.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.153
r_dihedral_angle_3_deg	15.63
r_dihedral_angle_4_deg	13.136
r_dihedral_angle_1_deg	9.087
r_lrange_other	5.84
r_lrange_it	5.81
r_scangle_it	4.398
r_scangle_other	4.398
r_mcangle_it	3.863
r_mcangle_other	3.863
r_scbond_it	3.064
r_scbond_other	3.064
r_mcbond_it	2.694
r_mcbond_other	2.684
r_angle_refined_deg	1.896
r_angle_other_deg	1.395
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.186
r_nbtor_refined	0.186
r_symmetry_nbd_other	0.185
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.11
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5986
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing