7Q20 | pdb_00007q20

Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) in complex with blood group A trisaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D6C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	12.5% MPD; 25% PEG 1000; 12.5% PEG 3350, 0.1 M Sodium HEPES/MOPS pH 7.5, 30 mM magnesium chloride hexahydrate and 30 mM calcium chloride dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.594	α = 90
b = 86.95	β = 100.33
c = 110.196	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 PILATUS 6M-F		2018-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99990	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	108.411	99.9	0.15	0.172	0.069	0.988	5.8	5.4		145680

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	97.7		1.748	1.931	0.808	0.394	1.1	5.4

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	4D6C	1.95	108.41	137854	7379	99.71	0.1866	0.18487	0.19	0.21883	0.22	RANDOM	42.812

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]
-1.75		1.25	0.59		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.125
r_dihedral_angle_4_deg	16.322
r_dihedral_angle_3_deg	12.663
r_long_range_B_refined	6.419
r_long_range_B_other	6.411
r_dihedral_angle_1_deg	6.331
r_scangle_other	2.733
r_mcangle_it	1.777
r_mcangle_other	1.777
r_scbond_it	1.711
r_scbond_other	1.711
r_angle_refined_deg	1.289
r_mcbond_it	1.13
r_mcbond_other	1.13
r_angle_other_deg	1.037
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13342
Nucleic Acid Atoms
Solvent Atoms	823
Heterogen Atoms	90

Software

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