6ZZR

The Crystal Structure of human LDHA from Biortus.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JNK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2830.2M Na malonate, 0.1M Bis-Tris propane pH6.5, 20% PEG3,350
Crystal Properties
Matthews coefficientSolvent content
2.3447.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.959α = 90
b = 66.479β = 100.097
c = 250.843γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6546.77197.90.1157.53.281570
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.70.529

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4jnk2.6546.7381522401297.4680.2160.21250.277148.316
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]
1.0793.0342.634-4.507
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.88
r_dihedral_angle_4_deg17.514
r_dihedral_angle_3_deg14.807
r_dihedral_angle_1_deg6.211
r_lrange_it4.018
r_lrange_other4.016
r_mcangle_it2.394
r_mcangle_other2.394
r_scangle_it2.04
r_scangle_other2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.88
r_dihedral_angle_4_deg17.514
r_dihedral_angle_3_deg14.807
r_dihedral_angle_1_deg6.211
r_lrange_it4.018
r_lrange_other4.016
r_mcangle_it2.394
r_mcangle_other2.394
r_scangle_it2.04
r_scangle_other2.04
r_mcbond_it1.395
r_mcbond_other1.395
r_angle_refined_deg1.19
r_scbond_it1.151
r_scbond_other1.151
r_angle_other_deg1.058
r_symmetry_xyhbond_nbd_refined0.27
r_symmetry_nbd_other0.17
r_nbd_refined0.164
r_symmetry_nbd_refined0.159
r_nbd_other0.15
r_nbtor_refined0.142
r_xyhbond_nbd_refined0.134
r_symmetry_nbtor_other0.073
r_chiral_restr0.039
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20503
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing