7EPS

Partial Consensus L-threonine 3-dehydrogenase (E-change)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WMX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20% [w/v] PEG 3350, 0.2M magnesium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.108	α = 90
b = 180.932	β = 90.007
c = 141.713	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2020-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	49.4	100	0.087	1	15.5	7		878278

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22			0.57	0.895

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3WMX	2.102	49.4	125517	6302	99.963	0.209	0.2072	0.2348	31.893

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]
2.362		0.103	-0.899		-1.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.557
r_dihedral_angle_4_deg	19.767
r_dihedral_angle_3_deg	14.502
r_dihedral_angle_1_deg	7.012
r_lrange_other	6.828
r_lrange_it	6.824
r_scangle_it	5.096
r_scangle_other	5.096
r_mcangle_it	3.966
r_mcangle_other	3.966
r_scbond_other	3.492
r_scbond_it	3.491
r_mcbond_it	2.959
r_mcbond_other	2.959
r_angle_refined_deg	1.607
r_angle_other_deg	1.406
r_symmetry_nbd_refined	0.541
r_nbd_other	0.439
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.186
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.104
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_6	0.081
r_ncsr_local_group_4	0.079
r_chiral_restr	0.078
r_ncsr_local_group_3	0.075
r_ncsr_local_group_1	0.074
r_xyhbond_nbd_other	0.063
r_ncsr_local_group_5	0.059
r_ncsr_local_group_2	0.052
r_bond_refined_d	0.011
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	9460
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	256

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing