8HP3

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M HEPES, pH 7.5, 0.1 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.73	α = 90
b = 189.6	β = 90
c = 101.82	γ = 90

Symmetry
Space Group	C 2 2 21

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	Bruker PHOTON II		2021-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.54178

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	3.07	47.53	99.8	0.173	7.8	4.7		18754

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	3.07	3.28			0.66

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.07	47.53	17866	870	99.63	0.2007	0.19786	0.26051	RANDOM	52.028

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]
-2.66			0.04		2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	20.002
r_dihedral_angle_3_deg	18.302
r_long_range_B_refined	9.711
r_long_range_B_other	9.71
r_dihedral_angle_1_deg	7.827
r_scangle_other	6.677
r_mcangle_it	6.134
r_mcangle_other	6.133
r_scbond_it	4.157
r_scbond_other	4.145
r_mcbond_it	3.885
r_mcbond_other	3.884
r_angle_refined_deg	1.485
r_angle_other_deg	1.157
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6804
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	220

Software

Software
Software Name	Purpose
Aimless	data scaling
HKL-2000	data reduction