8YHP

Structure of the PGK1 from Biortus.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Na/K PO4, 20% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.591	α = 90
b = 70.058	β = 90
c = 95.681	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 9M		2021-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.18075	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	47.84	99.8	0.094	12.9	6.1		30843

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.742

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.95	46.3	30812	1552	99.744	0.236	0.2337	0.2864	37.359

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]
-2.378			3.899		-1.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.974
r_dihedral_angle_3_deg	11.836
r_dihedral_angle_1_deg	5.795
r_dihedral_angle_2_deg	5.689
r_lrange_it	4.137
r_lrange_other	3.986
r_scangle_it	2.317
r_scangle_other	2.317
r_mcangle_it	2.228
r_mcangle_other	2.227
r_mcbond_it	1.343
r_mcbond_other	1.343
r_scbond_it	1.328
r_scbond_other	1.327
r_angle_refined_deg	0.898
r_angle_other_deg	0.326
r_nbd_refined	0.199
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.133
r_nbd_other	0.128
r_symmetry_nbtor_other	0.076
r_symmetry_nbd_refined	0.075
r_chiral_restr	0.043
r_symmetry_xyhbond_nbd_other	0.006
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3116
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	8

Software

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