7C27 | pdb_00007c27

Glycosidase F290Y at pH4.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Z3D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.811	α = 90
b = 104.811	β = 90
c = 90.158	γ = 90

Symmetry
Space Group	P 4 21 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 PILATUS3 S 2M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.91	46.92	99.9	0.238	0.242	0.998	0.107	26.4		39724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.02	99.8		3.651	3.722	0.429	0.01	26.7

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	FREE R-VALUE	5Z3D	1.91	46.92	39723	1992	99.942	0.183	0.1819	0.19	0.2117	0.22	36.2

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]
0.143			0.143		-0.286

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.762
r_dihedral_angle_4_deg	20.088
r_dihedral_angle_3_deg	13.339
r_lrange_it	6.485
r_lrange_other	6.334
r_dihedral_angle_1_deg	6.017
r_scangle_it	4.903
r_scangle_other	4.902
r_mcangle_other	3.787
r_mcangle_it	3.783
r_scbond_it	3.461
r_scbond_other	3.448
r_mcbond_it	2.863
r_mcbond_other	2.846
r_angle_refined_deg	1.623
r_angle_other_deg	1.449
r_symmetry_xyhbond_nbd_refined	0.227
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.182
r_nbd_other	0.182
r_chiral_restr_other	0.175
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.136
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_xyhbond_nbd_other	0.013
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2865
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	38

Software

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