7EPR | pdb_00007epr

Partial Consensus L-threonine 3-dehydrogenase (C-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		275	20% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.019	α = 90
b = 58.474	β = 92.234
c = 138.13	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		2019-12-06	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	2.2	46	99.9	0.074	0.999	16.3	6.8		412432

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	2.2	2.32			0.559	0.847

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	3WMX	2.2	46	60750	3100	99.859	0.211	0.2083	0.21	0.2582	0.26	47.019

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]
0.004		0.062	0.075		-0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.584
r_dihedral_angle_4_deg	20.163
r_dihedral_angle_3_deg	16.304
r_lrange_other	9.261
r_lrange_it	9.254
r_dihedral_angle_1_deg	6.91
r_scangle_it	6.484
r_scangle_other	6.484
r_mcangle_other	6.408
r_mcangle_it	6.407
r_mcbond_it	4.507
r_mcbond_other	4.503
r_scbond_it	4.41
r_scbond_other	4.409
r_angle_refined_deg	1.476
r_angle_other_deg	1.27
r_symmetry_xyhbond_nbd_refined	0.351
r_nbd_other	0.251
r_symmetry_xyhbond_nbd_other	0.234
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.162
r_ncsr_local_group_6	0.107
r_ncsr_local_group_4	0.104
r_ncsr_local_group_3	0.102
r_ncsr_local_group_2	0.1
r_ncsr_local_group_1	0.098
r_ncsr_local_group_5	0.098
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9335
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	176

Software

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