4LMR

Crystal structure of L-lactate dehydrogenase from Bacillus cereus ATCC 14579, NYSGRC Target 029452


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PQD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1M Tris-HCl, pH 8.5, 3.5M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.3972.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.276α = 90
b = 177.276β = 90
c = 168.975γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-04-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
12.45501000.08110.87.394016
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)
12.452.491000.6746.94686

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3PQD2.4546.7148772247099.210.16390.16310.1794RANDOM46.2424
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]
3.083.08-6.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.975
r_dihedral_angle_4_deg16.429
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg5.366
r_scbond_it3.723
r_mcangle_it3.638
r_mcbond_it2.243
r_angle_refined_deg1.239
r_chiral_restr0.088
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.975
r_dihedral_angle_4_deg16.429
r_dihedral_angle_3_deg15.209
r_dihedral_angle_1_deg5.366
r_scbond_it3.723
r_mcangle_it3.638
r_mcbond_it2.243
r_angle_refined_deg1.239
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4864
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction