6ZZR | pdb_00006zzr

The Crystal Structure of human LDHA from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JNK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283	0.2M Na malonate, 0.1M Bis-Tris propane pH6.5, 20% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.959	α = 90
b = 66.479	β = 100.097
c = 250.843	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		2020-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.65	46.771	97.9	0.115	7.5	3.2		81570

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	2.65	2.7			0.529

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	4jnk	2.65	46.73	81522	4012	97.468	0.216	0.2125	0.21	0.2771	0.27	48.316

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]
1.079		3.034	2.634		-4.507

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.88
r_dihedral_angle_4_deg	17.514
r_dihedral_angle_3_deg	14.807
r_dihedral_angle_1_deg	6.211
r_lrange_it	4.018
r_lrange_other	4.016
r_mcangle_it	2.394
r_mcangle_other	2.394
r_scangle_it	2.04
r_scangle_other	2.04
r_mcbond_it	1.395
r_mcbond_other	1.395
r_angle_refined_deg	1.19
r_scbond_it	1.151
r_scbond_other	1.151
r_angle_other_deg	1.058
r_symmetry_xyhbond_nbd_refined	0.27
r_symmetry_nbd_other	0.17
r_nbd_refined	0.164
r_symmetry_nbd_refined	0.159
r_nbd_other	0.15
r_nbtor_refined	0.142
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.039
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20503
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing