8Q1C | pdb_00008q1c

Substrate-free D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	0.6 mM bPGM-D10N,P146A 5 mM MgCl2 3 mM AlCl3 20 mM NaF 15 mM glucose 6-phosphate 32 % PEG 4000 200 mM sodium acetate 200 mM tris

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.65	α = 90
b = 117.251	β = 98.637
c = 53.25	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		2021-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	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	1.679	117.25	98.3	0.089	0.04	0.994	13.8	6.5		52374			28.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.71	86.9		0.277	0.6	5.7

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.679	52.702	52336	2655	98.202	0.214	0.2108	0.22	0.2702	0.28	39.612

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]
2.135		0.763	-1.294		-1.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.93
r_dihedral_angle_3_deg	14.471
r_dihedral_angle_2_deg	8.781
r_dihedral_angle_1_deg	6.149
r_angle_refined_deg	1.671
r_angle_other_deg	0.548
r_nbd_refined	0.232
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.151
r_nbd_other	0.151
r_symmetry_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.095
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3374
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	32

Software

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