6E85 | pdb_00006e85

1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-4-phosphate Dehydrogenase from Klebsiella pneumoniae.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HI1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 6.9 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.355	α = 90
b = 76.216	β = 106.78
c = 92.113	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	CCD	MARMOSAIC 300 mm CCD	C(111)	2018-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.25	30	99.8	0.053	0.053	0.06	0.028	24.6	4.3		177342		-3	12.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	97.7		0.549	0.549	0.654	0.349	0.8	2.3	3.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HI1	1.25	29.67	168266	8941	99.77	0.11509	0.11384	0.12	0.1392	0.14	RANDOM	16.874

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]
0.33		0.01	0.24		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.359
r_sphericity_free	19.899
r_dihedral_angle_4_deg	13.475
r_dihedral_angle_3_deg	11.275
r_rigid_bond_restr	8.784
r_sphericity_bonded	6.937
r_dihedral_angle_1_deg	4.679
r_long_range_B_refined	3.057
r_long_range_B_other	2.545
r_scangle_other	1.981
r_scbond_it	1.685
r_scbond_other	1.613
r_mcangle_it	1.458
r_mcangle_other	1.457
r_angle_refined_deg	1.283
r_mcbond_it	1.261
r_mcbond_other	1.261
r_angle_other_deg	0.489
r_chiral_restr	0.071
r_gen_planes_refined	0.042
r_gen_planes_other	0.04
r_bond_refined_d	0.006
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4923
Nucleic Acid Atoms
Solvent Atoms	954
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing