7DBJ

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	PEG 3350, potassium formate, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.389	α = 90
b = 137.577	β = 109.264
c = 84.909	γ = 90

Symmetry
Space Group	P 1 21 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 S 6M		2019-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rpim I (All)	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	1.55	50	99.2	0.076	0.042	0.989	20.3	4.1		183405

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	93.8		0.251	0.149	0.923	4	3.5

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	1I0Z	1.551	43.496	183364	9146	98.923	0.171	0.1697	0.1917	23.8

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]
-0.534		0.232	0.049		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.144
r_dihedral_angle_4_deg	19.508
r_dihedral_angle_3_deg	11.901
r_dihedral_angle_1_deg	6.418
r_lrange_it	3.065
r_lrange_other	3.058
r_angle_other_deg	1.6
r_dihedral_angle_other_2_deg	1.576
r_angle_refined_deg	1.549
r_scangle_it	1.247
r_scangle_other	1.247
r_scbond_it	0.969
r_scbond_other	0.969
r_mcangle_it	0.806
r_mcangle_other	0.806
r_mcbond_it	0.642
r_mcbond_other	0.64
r_nbd_other	0.263
r_nbd_refined	0.208
r_symmetry_nbd_other	0.186
r_symmetry_nbd_refined	0.177
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.011
r_bond_other_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10244
Nucleic Acid Atoms
Solvent Atoms	765
Heterogen Atoms	284

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing