8OZ1 | pdb_00008oz1

CjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	20 mg/mL enzyme in 50 mM NaPi pH 7.0 mixed 1:1 with 0.1 M MIB buffer, pH 4, 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.36	α = 90
b = 57.132	β = 98.528
c = 65.951	γ = 90

Symmetry
Space Group	P 1 21 1

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 XE 16M		2020-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.3	51.78	97.2	0.149	0.044	0.997	8.3	11.3		91883

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	75.3		1.113	0.542	0.577	0.9	5

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 (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	1.3	51.78	91862	4537	97.103	0.136	0.1344	0.14	0.1691	0.17	Random selection	16.393

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]
0.888		0.919	-1.644		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.515
r_dihedral_angle_3_deg	14.464
r_dihedral_angle_1_deg	6.916
r_dihedral_angle_2_deg	5.304
r_rigid_bond_restr	4.329
r_lrange_it	3.931
r_lrange_other	3.689
r_scangle_it	3.182
r_scangle_other	3.182
r_mcangle_other	2.622
r_mcangle_it	2.61
r_scbond_it	2.503
r_scbond_other	2.503
r_mcbond_it	2.084
r_mcbond_other	2.084
r_angle_refined_deg	1.741
r_angle_other_deg	0.733
r_symmetry_xyhbond_nbd_refined	0.282
r_nbd_refined	0.271
r_symmetry_nbd_other	0.218
r_nbtor_refined	0.183
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.118
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2954
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing