5OYD

GH5 endo-xyloglucanase from Cellvibrio japonicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OYC	5OYC.PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	ammonium sulphate, MES buffer

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.455	α = 90
b = 97.598	β = 90
c = 157.196	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	PIXEL	DECTRIS PILATUS 6M		2017-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97948	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.1	83.05	100	0.062	0.998	12.8	6.2		50763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	100		0.547	0.933		6.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5OYC.PDB	2.1	83.05	48113	2525	99.83	0.22106	0.21779	0.28293	RANDOM	48.033

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			3.89		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.13
r_dihedral_angle_4_deg	19.704
r_dihedral_angle_3_deg	14.994
r_dihedral_angle_1_deg	6.988
r_long_range_B_refined	6.833
r_long_range_B_other	6.833
r_scangle_other	5.556
r_mcangle_other	5.338
r_mcangle_it	5.336
r_scbond_it	4.262
r_scbond_other	4.259
r_mcbond_other	4.161
r_mcbond_it	4.16
r_angle_refined_deg	1.793
r_angle_other_deg	1.086
r_chiral_restr	0.104
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5792
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	178

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing