6YOZ | pdb_00006yoz

HiCel7B labelled with b-1,4-glucosyl cyclophellitol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	12 mg/mL protein in 20 mM pH 8 Tris buffer mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
4.1	69.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102	α = 90
b = 102	β = 90
c = 278.85	γ = 90

Symmetry
Space Group	P 41 2 2

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 EIGER2 X 16M		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.88	57.621	100	0.177	1	14.2	16.2		120246

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	100		2.978	0.5	1.1	16.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2A39	1.88	57.621	120246	5995	99.947	0.203	0.2018	0.21	0.2362	0.24	Random selection	33.48

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]
0.655			0.655		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.782
r_dihedral_angle_4_deg	14.702
r_dihedral_angle_3_deg	13.392
r_dihedral_angle_1_deg	7.37
r_lrange_it	6.464
r_lrange_other	6.403
r_scangle_other	5.517
r_scangle_it	5.516
r_scbond_it	3.938
r_scbond_other	3.938
r_mcangle_other	3.891
r_mcangle_it	3.887
r_mcbond_it	3.089
r_mcbond_other	3.081
r_angle_other_deg	2.457
r_angle_refined_deg	1.786
r_symmetry_nbd_refined	0.644
r_nbd_other	0.262
r_nbd_refined	0.226
r_symmetry_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_bond_other_d	0.036
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.013
r_gen_planes_other	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6100
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing