1GZ3

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DO8PDB ENTRY 1DO8_D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
169% PEG20K, PH 5.5 NA CITRATE, 5% MPD
Crystal Properties
Matthews coefficientSolvent content
3.0659.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.815α = 90
b = 192.653β = 89.77
c = 110.161γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002001-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8CNSLSX8C

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
12.320910.05182.125042921.4
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)
12.32.38780.08711

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DO8_D2.32021193258984910.1940.1940.233RANDOM27.2
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]
4.61-0.74-6.141.53
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_angle_deg1.3
c_improper_angle_d0.85
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_angle_deg1.3
c_improper_angle_d0.85
c_bond_d0.007
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
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17477
Nucleic Acid Atoms
Solvent Atoms1157
Heterogen Atoms184

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing