7DBK | pdb_00007dbk

Crystal structure of human LDHB in complex with NADH

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, ammonium acetate, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 232.477	α = 90
b = 84.173	β = 120.76
c = 156.21	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 S 6M		2020-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

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	1.8	50	99.6	0.065	0.042	0.994	19.8	3.4		237609

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	1.8	1.83	100		0.511	0.324	0.736	2.1

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	1I0Z	1.802	49.993	237609	11844	99.487	0.172	0.1702	0.18	0.2034	0.21	29.333

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]
-0.578		-0.04	0.336		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.572
r_dihedral_angle_4_deg	24.612
r_dihedral_angle_3_deg	14.82
r_dihedral_angle_1_deg	6.61
r_lrange_it	4.369
r_lrange_other	4.367
r_scangle_it	2.222
r_scangle_other	2.222
r_mcangle_it	1.664
r_mcangle_other	1.664
r_angle_refined_deg	1.548
r_scbond_it	1.414
r_scbond_other	1.414
r_angle_other_deg	1.373
r_mcbond_it	1.015
r_mcbond_other	1.015
r_symmetry_nbd_refined	0.257
r_nbd_refined	0.2
r_nbd_other	0.194
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.066
r_bond_refined_d	0.01
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	20488
Nucleic Acid Atoms
Solvent Atoms	977
Heterogen Atoms	484

Software

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