1H12 | pdb_00001h12

Structure of a cold-adapted family 8 xylanase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		WILD TYPE WITHOUT LIGAND

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS, 50MM NACL, 2% TREHALOSE, PH 7.5. ADD EQUAL VOLUME OF 70% MPD, 0.1M PHOSPHATE BUFFER PH 7.0 WITH 10MG/ML XYLOBIOSE IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE.

Crystal Properties
Matthews coefficient	Solvent content
2.43	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.972	α = 90
b = 90.734	β = 90
c = 97.581	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	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

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	1.2	20	99.4	0.032	43.52	5		141707		2

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	1.2	1.22	91.9		0.235	3.69	2.5

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 (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	WILD TYPE WITHOUT LIGAND	1.2	65.94	133682	7056	99.3	0.108	0.107	0.13	0.13	0.15	RANDOM	10.66

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]
-0.22			0.36		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.623
r_dihedral_angle_1_deg	5.866
r_scangle_it	5.613
r_scbond_it	3.882
r_angle_other_deg	3.483
r_mcangle_it	2.441
r_angle_refined_deg	1.816
r_mcbond_it	1.684
r_nbtor_other	0.371
r_symmetry_vdw_refined	0.275
r_symmetry_vdw_other	0.265
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.202
r_nbd_other	0.197
r_chiral_restr	0.196
r_symmetry_hbond_refined	0.194
r_bond_refined_d	0.029
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3203
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	20

Software

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