1IZ9

Crystal Structure of Malate Dehydrogenase from Thermus thermophilus HB8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMDPDB ENTRY 1BMD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG MME 2000, Nickel Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.64α = 90
b = 88.03β = 90
c = 118.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS VIIOsmic Confocal Max-Flux Optics2002-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
1270.7199.50.0845.85106651066521.8
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)
22.0798.70.3941.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BMD219.925114051066254599.30.1930.1930.1930.226RANDOM35.8
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]
3.61-1.64-1.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it3.68
c_scbond_it2.41
c_mcangle_it2.09
c_mcbond_it1.33
c_angle_deg1.2
c_improper_angle_d0.82
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it3.68
c_scbond_it2.41
c_mcangle_it2.09
c_mcbond_it1.33
c_angle_deg1.2
c_improper_angle_d0.82
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4978
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
AMoREphasing
CNSrefinement
CrystalCleardata scaling